rs62637580

Positions:

chr9-133352739-G-A

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_003172.4(SURF1):c.543C>T(p.Phe181=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0091 in 1,612,502 control chromosomes in the GnomAD database, including 1,267 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.013 ( 141 hom., cov: 33)

Exomes 𝑓: 0.0087 ( 1126 hom. )

Consequence

SURF1
NM_003172.4 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 1.26

Variant links:

Genes affected

SURF1 (HGNC:11474): (SURF1 cytochrome c oxidase assembly factor) This gene encodes a protein localized to the inner mitochondrial membrane and thought to be involved in the biogenesis of the cytochrome c oxidase complex. The protein is a member of the SURF1 family, which includes the related yeast protein SHY1 and rickettsial protein RP733. The gene is located in the surfeit gene cluster, a group of very tightly linked genes that do not share sequence similarity, where it shares a bidirectional promoter with SURF2 on the opposite strand. Defects in this gene are a cause of Leigh syndrome, a severe neurological disorder that is commonly associated with systemic cytochrome c oxidase deficiency. [provided by RefSeq, Jul 2008]

SURF1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 9-133352739-G-A is Benign according to our data. Variant chr9-133352739-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 215225.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-133352739-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SURF1	NM_003172.4 linkuse as main transcript	c.543C>T	p.Phe181=	synonymous_variant	6/9	ENST00000371974.8	NP_003163.1
SURF1	NM_001280787.1 linkuse as main transcript	c.216C>T	p.Phe72=	synonymous_variant	5/8		NP_001267716.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SURF1	ENST00000371974.8 linkuse as main transcript	c.543C>T	p.Phe181=	synonymous_variant	6/9	1	NM_003172.4	ENSP00000361042	P1	Q15526-1
SURF1	ENST00000615505.4 linkuse as main transcript	c.216C>T	p.Phe72=	synonymous_variant	5/8	1		ENSP00000482067
SURF1	ENST00000495952.5 linkuse as main transcript	n.533C>T		non_coding_transcript_exon_variant	2/5	2
SURF1	ENST00000437995.1 linkuse as main transcript	n.462-9C>T		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.0131

AC:

1997

AN:

152204

Hom.:

141

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0123

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00412

Gnomad ASJ

AF:

0.00922

Gnomad EAS

AF:

0.229

Gnomad SAS

AF:

0.0161

Gnomad FIN

AF:

0.000471

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00135

Gnomad OTH

AF:

0.0124

GnomAD3 exomes

AF:

0.0209

AC:

5185

AN:

248436

Hom.:

498

AF XY:

0.0197

AC XY:

2651

AN XY:

134500

show subpopulations

Gnomad AFR exome

AF:

0.0139

Gnomad AMR exome

AF:

0.00204

Gnomad ASJ exome

AF:

0.00975

Gnomad EAS exome

AF:

0.233

Gnomad SAS exome

AF:

0.0104

Gnomad FIN exome

AF:

0.000186

Gnomad NFE exome

AF:

0.00151

Gnomad OTH exome

AF:

0.0107

GnomAD4 exome

AF:

0.00868

AC:

12676

AN:

1460182

Hom.:

1126

Cov.:

AF XY:

0.00876

AC XY:

6365

AN XY:

726284

show subpopulations

Gnomad4 AFR exome

AF:

0.0137

Gnomad4 AMR exome

AF:

0.00220

Gnomad4 ASJ exome

AF:

0.00989

Gnomad4 EAS exome

AF:

0.227

Gnomad4 SAS exome

AF:

0.0112

Gnomad4 FIN exome

AF:

0.000319

Gnomad4 NFE exome

AF:

0.000904

Gnomad4 OTH exome

AF:

0.0138

GnomAD4 genome

AF:

0.0132

AC:

2004

AN:

152320

Hom.:

141

Cov.:

AF XY:

0.0143

AC XY:

1066

AN XY:

74480

show subpopulations

Gnomad4 AFR

AF:

0.0124

Gnomad4 AMR

AF:

0.00412

Gnomad4 ASJ

AF:

0.00922

Gnomad4 EAS

AF:

0.229

Gnomad4 SAS

AF:

0.0170

Gnomad4 FIN

AF:

0.000471

Gnomad4 NFE

AF:

0.00135

Gnomad4 OTH

AF:

0.0123

Alfa

AF:

0.00569

Hom.:

Bravo

AF:

0.0167

Asia WGS

AF:

0.0800

AC:

278

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, no assertion criteria provided	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Feb 29, 2016	- -
Benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Apr 05, 2016	Variant summary: The c.543C>T in SURF1 gene is a synonymous change that involves a non-conserved nucleotide. 5/5 programs in Alamut predict that this variant does not affect normal splicing, however no functional studies supporting this notion were published at the time of evaluation. The variant is present in the control population dataset of ExAC at frequency of 2%, primarily in individuals of East Asian descent (~26%), including numerous homozygous occurrences. The observed frequency exceeds the maximum expected allele frequency for a pathogenic SURF1 variant, suggesting that it is a common polymorphism. In addition, the variant has been reported as Benign by reputable database/clinical laboratory. Taken together, this variant has been classified as Benign. -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Leigh syndrome

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jun 14, 2016	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 05, 2011

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

5.0

DANN

Benign

0.79

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.32

Details are displayed if max score is > 0.2

DS_AL_spliceai

0.32

Position offset: 27

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over