20-3858160-C-T

Position:

• chr20-3858160-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
MAVS	NM_020746.5	c.292+351C>T		intron_variant		ENST00000428216.4	NP_065797.2
MAVS	NM_001206491.2	c.-131-3172C>T		intron_variant			NP_001193420.1
MAVS	NM_001385663.1	c.-256+351C>T		intron_variant			NP_001372592.1
MAVS	NR_037921.2	n.429+351C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAVS	ENST00000428216.4	c.292+351C>T		intron_variant		1	NM_020746.5	ENSP00000401980.2
MAVS	ENST00000416600.6	c.-131-3172C>T		intron_variant		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

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.654

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.328

Alfa AF: 0.264 Hom.: 6556

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

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

Other links and lift over

dbSNP: rs8116776; hg19: chr20-3838807;