Variant 2-190436914-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_017694.4(MFSD6):c.885C>T(p.Val295=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0108 in 1,614,172 control chromosomes in the GnomAD database, including 118 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0077 ( 5 hom., cov: 32)

Exomes 𝑓: 0.011 ( 113 hom. )

Consequence

MFSD6
NM_017694.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.680

Variant links:

Genes affected

MFSD6 (HGNC:24711): (major facilitator superfamily domain containing 6) Predicted to enable MHC class I protein binding activity and MHC class I receptor activity. Predicted to be involved in antigen processing and presentation of exogenous peptide antigen via MHC class I. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

MFSD6 links:

NEMP2 (HGNC:):

NEMP2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.42).

BP6

Variant 2-190436914-C-T is Benign according to our data. Variant chr2-190436914-C-T is described in ClinVar as [Benign]. Clinvar id is 777960.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.68 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MFSD6	NM_017694.4 linkuse as main transcript	c.885C>T	p.Val295=	synonymous_variant	3/8	ENST00000392328.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MFSD6	ENST00000392328.6 linkuse as main transcript	c.885C>T	p.Val295=	synonymous_variant	3/8	2	NM_017694.4	P1
MFSD6	ENST00000281416.11 linkuse as main transcript	c.885C>T	p.Val295=	synonymous_variant	1/6	1		P1

Frequencies

GnomAD3 genomes

AF:

0.00775

AC:

1180

AN:

152186

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00188

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.00511

Gnomad ASJ

AF:

0.0550

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00165

Gnomad FIN

AF:

0.00509

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0109

Gnomad OTH

AF:

0.0105

GnomAD3 exomes

AF:

0.00846

AC:

2127

AN:

251492

Hom.:

AF XY:

0.00852

AC XY:

1158

AN XY:

135920

show subpopulations

Gnomad AFR exome

AF:

0.00252

Gnomad AMR exome

AF:

0.00396

Gnomad ASJ exome

AF:

0.0433

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00304

Gnomad FIN exome

AF:

0.00513

Gnomad NFE exome

AF:

0.0110

Gnomad OTH exome

AF:

0.00993

GnomAD4 exome

AF:

0.0111

AC:

16193

AN:

1461868

Hom.:

113

Cov.:

AF XY:

0.0108

AC XY:

7872

AN XY:

727234

show subpopulations

Gnomad4 AFR exome

AF:

0.00185

Gnomad4 AMR exome

AF:

0.00429

Gnomad4 ASJ exome

AF:

0.0425

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00311

Gnomad4 FIN exome

AF:

0.00483

Gnomad4 NFE exome

AF:

0.0121

Gnomad4 OTH exome

AF:

0.0129

GnomAD4 genome

AF:

0.00774

AC:

1179

AN:

152304

Hom.:

Cov.:

AF XY:

0.00733

AC XY:

546

AN XY:

74472

show subpopulations

Gnomad4 AFR

AF:

0.00188

Gnomad4 AMR

AF:

0.00510

Gnomad4 ASJ

AF:

0.0550

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.00509

Gnomad4 NFE

AF:

0.0109

Gnomad4 OTH

AF:

0.00993

Alfa

AF:

0.0121

Hom.:

Bravo

AF:

0.00789

Asia WGS

AF:

0.00173

AC:

AN:

3478

EpiCase

AF:

0.0125

EpiControl

AF:

0.0124

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

Invitae

Mar 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.42

CADD

Benign

5.8

DANN

Benign

0.68

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