chr20-3858160-C-T

Variant names:

• chr20-3858160-C-T
• rs8116776
• NM_020746.5:c.292+351C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020746.5(MAVS):​c.292+351C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 151,824 control chromosomes in the GnomAD database, including 8,492 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.

• Frequency: Genomes: 𝑓 0.32 (8492 hom., cov: 30)
• Consequence: MAVS NM_020746.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230
• Publications: 13 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAVS	NM_020746.5	c.292+351C>T		intron_variant	Intron 3 of 6	ENST00000428216.4	NP_065797.2
MAVS	NM_001206491.2	c.-131-3172C>T		intron_variant	Intron 2 of 5		NP_001193420.1
MAVS	NM_001385663.1	c.-256+351C>T		intron_variant	Intron 3 of 7		NP_001372592.1
MAVS	NR_037921.2	n.429+351C>T		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAVS	ENST00000428216.4	c.292+351C>T		intron_variant	Intron 3 of 6	1	NM_020746.5	ENSP00000401980.2
MAVS	ENST00000416600.6	c.-131-3172C>T		intron_variant	Intron 2 of 5	1		ENSP00000413749.2

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48381 AN: 151706 Hom.: 8483 Cov.: 30

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.331

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.319 AC: 48419 AN: 151824 Hom.: 8492 Cov.: 30 AF XY: 0.323 AC XY: 23995 AN XY: 74192

African (AFR) AF: 0.419 AC: 17355 AN: 41382

American (AMR) AF: 0.314 AC: 4782 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 728 AN: 3472

East Asian (EAS) AF: 0.654 AC: 3342 AN: 5110

South Asian (SAS) AF: 0.384 AC: 1852 AN: 4820

European-Finnish (FIN) AF: 0.250 AC: 2645 AN: 10576

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16768 AN: 67918

Other (OTH) AF: 0.328 AC: 689 AN: 2102

Alfa AF: 0.281 Hom.: 11207

Bravo AF: 0.331

Asia WGS AF: 0.486 AC: 1688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.47
PhyloP100		0.23
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs8116776; hg19: chr20-3838807;