Variant 6-158158205-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_032861.4(SERAC1):c.91+68A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 1,203,186 control chromosomes in the GnomAD database, including 55,617 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.31 ( 7674 hom., cov: 31)

Exomes 𝑓: 0.29 ( 47943 hom. )

Consequence

SERAC1
NM_032861.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0600

Variant links:

Genes affected

SERAC1 (HGNC:21061): (serine active site containing 1) The protein encoded by this gene is a phosphatidylglycerol remodeling protein found at the interface of mitochondria and endoplasmic reticula, where it mediates phospholipid exchange. The encoded protein plays a major role in mitochondrial function and intracellular cholesterol trafficking. Defects in this gene are a cause of 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome (MEGDEL). Two transcript variants, one protein-coding and the other non-protein coding, have been found for this gene. [provided by RefSeq, Aug 2012]

SERAC1 links:

SERAC1 (HGNC:):

SERAC1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 6-158158205-T-C is Benign according to our data. Variant chr6-158158205-T-C is described in ClinVar as [Benign]. Clinvar id is 671613.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SERAC1	NM_032861.4 linkuse as main transcript	c.91+68A>G		intron_variant		ENST00000647468.2	NP_116250.3	Q96JX3-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SERAC1	ENST00000647468.2 linkuse as main transcript	c.91+68A>G		intron_variant			NM_032861.4	ENSP00000496731.1		Q96JX3-1

Frequencies

GnomAD3 genomes

AF:

0.311

AC:

47184

AN:

151852

Hom.:

7639

Cov.:

show subpopulations

Gnomad AFR

AF:

0.332

Gnomad AMI

AF:

0.121

Gnomad AMR

AF:

0.448

Gnomad ASJ

AF:

0.226

Gnomad EAS

AF:

0.425

Gnomad SAS

AF:

0.281

Gnomad FIN

AF:

0.290

Gnomad MID

AF:

0.285

Gnomad NFE

AF:

0.271

Gnomad OTH

AF:

0.294

GnomAD4 exome

AF:

0.292

AC:

307148

AN:

1051216

Hom.:

47943

AF XY:

0.290

AC XY:

155212

AN XY:

535294

show subpopulations

Gnomad4 AFR exome

AF:

0.334

Gnomad4 AMR exome

AF:

0.554

Gnomad4 ASJ exome

AF:

0.244

Gnomad4 EAS exome

AF:

0.492

Gnomad4 SAS exome

AF:

0.280

Gnomad4 FIN exome

AF:

0.304

Gnomad4 NFE exome

AF:

0.273

Gnomad4 OTH exome

AF:

0.285

GnomAD4 genome

AF:

0.311

AC:

47261

AN:

151970

Hom.:

7674

Cov.:

AF XY:

0.314

AC XY:

23359

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.333

Gnomad4 AMR

AF:

0.449

Gnomad4 ASJ

AF:

0.226

Gnomad4 EAS

AF:

0.425

Gnomad4 SAS

AF:

0.282

Gnomad4 FIN

AF:

0.290

Gnomad4 NFE

AF:

0.271

Gnomad4 OTH

AF:

0.298

Alfa

AF:

0.299

Hom.:

1014

Bravo

AF:

0.325

Asia WGS

AF:

0.347

AC:

1203

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 14, 2018

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

-0.90

CADD

Benign

1.5

DANN

Benign

0.61

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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