20-3849815-C-T

Position:

• chr20-3849815-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.-68+2912C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0657 in 152,196 control chromosomes in the GnomAD database, including 478 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 0.066 (478 hom., cov: 32)
• Consequence: MAVS NM_020746.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.897

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAVS	NM_020746.5	c.-68+2912C>T		intron_variant		ENST00000428216.4	NP_065797.2
MAVS	NM_001206491.2	c.-316+2912C>T		intron_variant			NP_001193420.1
MAVS	NM_001385663.1	c.-615+2912C>T		intron_variant			NP_001372592.1
MAVS	NR_037921.2	n.70+2912C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAVS	ENST00000428216.4	c.-68+2912C>T		intron_variant		1	NM_020746.5	ENSP00000401980.2
MAVS	ENST00000416600.6	c.-316+2912C>T		intron_variant		1		ENSP00000413749.2

Frequencies

GnomAD3 genomes AF: 0.0656 AC: 9975 AN: 152078 Hom.: 476 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0338

Gnomad ASJ AF: 0.0565

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.0769

Gnomad FIN AF: 0.0576

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0312

Gnomad OTH AF: 0.0698

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

GnomAD4 genome AF: 0.0657 AC: 9992 AN: 152196 Hom.: 478 Cov.: 32 AF XY: 0.0670 AC XY: 4987 AN XY: 74416

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.0339

Gnomad4 ASJ AF: 0.0565

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.0776

Gnomad4 FIN AF: 0.0576

Gnomad4 NFE AF: 0.0312

Gnomad4 OTH AF: 0.0700

Alfa AF: 0.0330 Hom.: 92

Bravo AF: 0.0671

Asia WGS AF: 0.103 AC: 357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.32
DANN	Benign	0.45

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: rs6084496; hg19: chr20-3830462;