rs6116065

Variant names:

• chr20-3849020-G-A
• rs6116065
• NM_020746.5:c.-68+2117G>A

Your query was ambiguous. Multiple possible variants found:

• chr20-3849020-G-A
• chr20-3849020-G-C
• chr20-3849020-G-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.-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
• Publications: 11 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020746.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAVS	NM_020746.5	MANE Select	c.-68+2117G>A		intron	N/A	NP_065797.2	Q7Z434-1
	MAVS	NM_001206491.2		c.-316+2117G>A		intron	N/A	NP_001193420.1	Q7Z434-4
	MAVS	NM_001385663.1		c.-615+2117G>A		intron	N/A	NP_001372592.1	Q7Z434-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAVS	ENST00000428216.4	TSL:1 MANE Select	c.-68+2117G>A		intron	N/A	ENSP00000401980.2	Q7Z434-1
	MAVS	ENST00000416600.6	TSL:1	c.-316+2117G>A		intron	N/A	ENSP00000413749.2	Q7Z434-4
	MAVS	ENST00000883969.1		c.-202+2117G>A		intron	N/A	ENSP00000554028.1

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

African (AFR) AF: 0.354 AC: 14630 AN: 41382

American (AMR) AF: 0.370 AC: 5638 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 893 AN: 3470

East Asian (EAS) AF: 0.674 AC: 3473 AN: 5156

South Asian (SAS) AF: 0.476 AC: 2279 AN: 4788

European-Finnish (FIN) AF: 0.406 AC: 4273 AN: 10532

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21936 AN: 67906

Other (OTH) AF: 0.375 AC: 789 AN: 2102

Alfa AF: 0.336 Hom.: 16519

Bravo AF: 0.356

Asia WGS AF: 0.560 AC: 1944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.9
DANN	Benign	0.79
PhyloP100		0.41
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: rs6116065; hg19: chr20-3829667;