rs6037678

Positions:

• chr20-3851613-C-G
• chr20-3851613-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.-67-2945C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0699 in 151,966 control chromosomes in the GnomAD database, including 554 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 0.070 (554 hom., cov: 31)
• Consequence: MAVS NM_020746.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAVS	NM_020746.5	c.-67-2945C>G		intron_variant		ENST00000428216.4	NP_065797.2
MAVS	NM_001206491.2	c.-315-2945C>G		intron_variant			NP_001193420.1
MAVS	NM_001385663.1	c.-614-2945C>G		intron_variant			NP_001372592.1
MAVS	NR_037921.2	n.71-2945C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAVS	ENST00000428216.4	c.-67-2945C>G		intron_variant		1	NM_020746.5	ENSP00000401980.2
MAVS	ENST00000416600.6	c.-315-2945C>G		intron_variant		1		ENSP00000413749.2

Frequencies

GnomAD3 genomes AF: 0.0698 AC: 10598 AN: 151846 Hom.: 550 Cov.: 31

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0361

Gnomad ASJ AF: 0.0568

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0916

Gnomad FIN AF: 0.0574

Gnomad MID AF: 0.0673

Gnomad NFE AF: 0.0327

Gnomad OTH AF: 0.0733

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

GnomAD4 genome AF: 0.0699 AC: 10624 AN: 151966 Hom.: 554 Cov.: 31 AF XY: 0.0715 AC XY: 5307 AN XY: 74274

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.0361

Gnomad4 ASJ AF: 0.0568

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.0923

Gnomad4 FIN AF: 0.0574

Gnomad4 NFE AF: 0.0327

Gnomad4 OTH AF: 0.0735

Alfa AF: 0.0223 Hom.: 13

Bravo AF: 0.0716

Asia WGS AF: 0.109 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	7.8
DANN	Benign	0.89

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: rs6037678; hg19: chr20-3832260;