chr20-3849020-G-A

Position:

• chr20-3849020-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020746.5(MAVS):​c.-68+2117G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,790 control chromosomes in the GnomAD database, including 10,106 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 0.36 (10106 hom., cov: 30)
• Consequence: MAVS NM_020746.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAVS	NM_020746.5	c.-68+2117G>A		intron_variant		ENST00000428216.4	NP_065797.2
MAVS	NM_001206491.2	c.-316+2117G>A		intron_variant			NP_001193420.1
MAVS	NM_001385663.1	c.-615+2117G>A		intron_variant			NP_001372592.1
MAVS	NR_037921.2	n.70+2117G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAVS	ENST00000428216.4	c.-68+2117G>A		intron_variant		1	NM_020746.5	ENSP00000401980	P1
MAVS	ENST00000416600.6	c.-316+2117G>A		intron_variant		1		ENSP00000413749

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54058 AN: 151672 Hom.: 10087 Cov.: 30

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.357 AC: 54119 AN: 151790 Hom.: 10106 Cov.: 30 AF XY: 0.364 AC XY: 26998 AN XY: 74172

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.674

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.375

Alfa AF: 0.332 Hom.: 11598

Bravo AF: 0.356

Asia WGS AF: 0.560 AC: 1944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.9
DANN	Benign	0.79

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: rs6116065; hg19: chr20-3829667;