Variant rs7262903 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020746.5(MAVS):c.592C>A(p.Gln198Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 1,613,710 control chromosomes in the GnomAD database, including 19,824 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.16 ( 1973 hom., cov: 33)

Exomes 𝑓: 0.15 ( 17851 hom. )

Consequence

MAVS
NM_020746.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.223

Variant links:

Genes affected

MAVS (HGNC:29233): (mitochondrial antiviral signaling protein) This gene encodes an intermediary protein necessary in the virus-triggered beta interferon signaling pathways. It is required for activation of transcription factors which regulate expression of beta interferon and contributes to antiviral innate immunity. [provided by RefSeq, Jul 2020]

MAVS links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.001180917).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
MAVS	NM_020746.5 linkuse as main transcript	c.592C>A	p.Gln198Lys	missense_variant	5/7	ENST00000428216.4
MAVS	NM_001206491.2 linkuse as main transcript	c.169C>A	p.Gln57Lys	missense_variant	4/6
MAVS	NM_001385663.1 linkuse as main transcript	c.169C>A	p.Gln57Lys	missense_variant	6/8
MAVS	NR_037921.2 linkuse as main transcript	n.556C>A		non_coding_transcript_exon_variant	4/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAVS	ENST00000428216.4 linkuse as main transcript	c.592C>A	p.Gln198Lys	missense_variant	5/7	1	NM_020746.5	P1	Q7Z434-1
MAVS	ENST00000416600.6 linkuse as main transcript	c.169C>A	p.Gln57Lys	missense_variant	4/6	1			Q7Z434-4

Frequencies

GnomAD3 genomes

AF:

0.158

AC:

24048

AN:

152038

Hom.:

1973

Cov.:

show subpopulations

Gnomad AFR

AF:

0.189

Gnomad AMI

AF:

0.0815

Gnomad AMR

AF:

0.136

Gnomad ASJ

AF:

0.158

Gnomad EAS

AF:

0.0890

Gnomad SAS

AF:

0.180

Gnomad FIN

AF:

0.108

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.157

Gnomad OTH

AF:

0.166

GnomAD3 exomes

AF:

0.145

AC:

36292

AN:

251024

Hom.:

2852

AF XY:

0.148

AC XY:

20107

AN XY:

135696

show subpopulations

Gnomad AFR exome

AF:

0.189

Gnomad AMR exome

AF:

0.0932

Gnomad ASJ exome

AF:

0.178

Gnomad EAS exome

AF:

0.103

Gnomad SAS exome

AF:

0.177

Gnomad FIN exome

AF:

0.113

Gnomad NFE exome

AF:

0.154

Gnomad OTH exome

AF:

0.159

GnomAD4 exome

AF:

0.153

AC:

223649

AN:

1461554

Hom.:

17851

Cov.:

AF XY:

0.154

AC XY:

112273

AN XY:

727088

show subpopulations

Gnomad4 AFR exome

AF:

0.191

Gnomad4 AMR exome

AF:

0.0975

Gnomad4 ASJ exome

AF:

0.168

Gnomad4 EAS exome

AF:

0.111

Gnomad4 SAS exome

AF:

0.177

Gnomad4 FIN exome

AF:

0.114

Gnomad4 NFE exome

AF:

0.155

Gnomad4 OTH exome

AF:

0.156

GnomAD4 genome

AF:

0.158

AC:

24060

AN:

152156

Hom.:

1973

Cov.:

AF XY:

0.155

AC XY:

11568

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.189

Gnomad4 AMR

AF:

0.136

Gnomad4 ASJ

AF:

0.158

Gnomad4 EAS

AF:

0.0890

Gnomad4 SAS

AF:

0.179

Gnomad4 FIN

AF:

0.108

Gnomad4 NFE

AF:

0.157

Gnomad4 OTH

AF:

0.165

Alfa

AF:

0.155

Hom.:

4527

Bravo

AF:

0.160

TwinsUK

AF:

0.162

AC:

599

ALSPAC

AF:

0.137

AC:

529

ESP6500AA

AF:

0.187

AC:

825

ESP6500EA

AF:

0.162

AC:

1396

ExAC

AF:

0.148

AC:

17984

Asia WGS

AF:

0.127

AC:

445

AN:

3478

EpiCase

AF:

0.163

EpiControl

AF:

0.160

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.077

BayesDel_addAF

Benign

-0.68

BayesDel_noAF

Benign

-0.61

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.17

.;T

Eigen

Benign

-0.22

Eigen_PC

Benign

-0.36

FATHMM_MKL

Benign

0.16

LIST_S2

Benign

0.68

T;T

MetaRNN

Benign

0.0012

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.1

.;M

MutationTaster

Benign

1.0

P;P;P

PrimateAI

Benign

0.30

PROVEAN

Uncertain

-3.5

D;N

REVEL

Benign

0.064

Sift

Benign

0.055

T;D

Sift4G

Benign

0.19

T;T

Polyphen

0.98

.;D

Vest4

0.24

MPC

0.32

ClinPred

0.034

GERP RS

1.1

Varity_R

0.11

gMVP

0.21

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over