Variant 9-133356715-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_017503.5(SURF2):c.78+45T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000765 in 1,480,164 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0043 ( 8 hom., cov: 31)

Exomes 𝑓: 0.00038 ( 5 hom. )

Consequence

SURF2
NM_017503.5 intron

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.389

Variant links:

Genes affected

SURF2 (HGNC:11475): (surfeit 2) This gene shares a bidirectional promoter with surfeit 1 (SURF1; GeneID: 6834), which is located on the opposite strand. It encodes a conserved protein that is expressed in a variety of tissues. [provided by RefSeq, Jul 2013]

SURF2 links:

SURF2 (HGNC:):

SURF2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 9-133356715-T-C is Benign according to our data. Variant chr9-133356715-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1219076.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SURF2	NM_017503.5 linkuse as main transcript	c.78+45T>C		intron_variant		ENST00000371964.5	NP_059973.4	Q15527
SURF2	NM_001278928.2 linkuse as main transcript	c.78+45T>C		intron_variant			NP_001265857.1	Q15527

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
SURF2	ENST00000371964.5 linkuse as main transcript	c.78+45T>C	intron_variant	1	NM_017503.5	ENSP00000361032.4	Q15527
SURF2	ENST00000495524.5 linkuse as main transcript	n.93+45T>C	intron_variant	5
SURF1	ENST00000463965.1 linkuse as main transcript	n.-39A>G	upstream_gene_variant	3

Frequencies

GnomAD3 genomes

AF:

0.00426

AC:

633

AN:

148514

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0153

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000799

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000216

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000448

Gnomad OTH

AF:

0.00148

GnomAD3 exomes

AF:

0.000659

AC:

AN:

85008

Hom.:

AF XY:

0.000446

AC XY:

AN XY:

47132

show subpopulations

Gnomad AFR exome

AF:

0.0158

Gnomad AMR exome

AF:

0.000426

Gnomad ASJ exome

AF:

0.000190

Gnomad EAS exome

AF:

0.000165

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.000376

GnomAD4 exome

AF:

0.000376

AC:

500

AN:

1331542

Hom.:

Cov.:

AF XY:

0.000283

AC XY:

185

AN XY:

653948

show subpopulations

Gnomad4 AFR exome

AF:

0.0150

Gnomad4 AMR exome

AF:

0.000545

Gnomad4 ASJ exome

AF:

0.0000443

Gnomad4 EAS exome

AF:

0.0000314

Gnomad4 SAS exome

AF:

0.0000409

Gnomad4 FIN exome

AF:

0.0000310

Gnomad4 NFE exome

AF:

0.00000475

Gnomad4 OTH exome

AF:

0.000830

GnomAD4 genome

AF:

0.00426

AC:

633

AN:

148622

Hom.:

Cov.:

AF XY:

0.00402

AC XY:

291

AN XY:

72380

show subpopulations

Gnomad4 AFR

AF:

0.0152

Gnomad4 AMR

AF:

0.000798

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000216

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000448

Gnomad4 OTH

AF:

0.00147

Alfa

AF:

0.00455

Hom.:

Bravo

AF:

0.00456

Asia WGS

AF:

0.000866

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Oct 07, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

4.5

DANN

Benign

0.77

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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