dbSNP rs6515831: MAVS:c.*5157T>C (chr20-3871304-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020746.5(MAVS):c.*5157T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 153,774 control chromosomes in the GnomAD database, including 11,452 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 ( 11275 hom., cov: 32)

Exomes 𝑓: 0.46 ( 177 hom. )

Consequence

MAVS
NM_020746.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.882

Publications

14 publications found

Variant links:

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 links:

PANK2-AS1 (HGNC:40732): (PANK2 antisense RNA 1)

PANK2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.456 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MAVS	NM_020746.5	MANE Select	c.*5157T>C	3_prime_UTR	Exon 7 of 7	NP_065797.2	Q7Z434-1
MAVS	NM_001206491.2		c.*5157T>C	3_prime_UTR	Exon 6 of 6	NP_001193420.1	Q7Z434-4
MAVS	NM_001385663.1		c.*5157T>C	3_prime_UTR	Exon 8 of 8	NP_001372592.1	Q7Z434-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MAVS	ENST00000428216.4	TSL:1 MANE Select	c.*5157T>C	3_prime_UTR	Exon 7 of 7	ENSP00000401980.2	Q7Z434-1
MAVS	ENST00000416600.6	TSL:1	c.*5157T>C	3_prime_UTR	Exon 6 of 6	ENSP00000413749.2	Q7Z434-4
PANK2-AS1	ENST00000725518.1		n.426-8414A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.361

AC:

54913

AN:

151958

Hom.:

11271

Cov.:

show subpopulations

Gnomad AFR

AF:

0.160

Gnomad AMI

AF:

0.546

Gnomad AMR

AF:

0.406

Gnomad ASJ

AF:

0.375

Gnomad EAS

AF:

0.225

Gnomad SAS

AF:

0.395

Gnomad FIN

AF:

0.477

Gnomad MID

AF:

0.408

Gnomad NFE

AF:

0.460

Gnomad OTH

AF:

0.374

GnomAD4 exome

AF:

0.463

AC:

786

AN:

1698

Hom.:

177

Cov.:

AF XY:

0.431

AC XY:

383

AN XY:

888

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.423

AC:

AN:

130

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.465

AC:

711

AN:

1528

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.545

AC:

AN:

Other (OTH)

AF:

0.438

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

112

140

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.361

AC:

54922

AN:

152076

Hom.:

11275

Cov.:

AF XY:

0.362

AC XY:

26883

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.160

AC:

6627

AN:

41516

American (AMR)

AF:

0.407

AC:

6200

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.375

AC:

1299

AN:

3466

East Asian (EAS)

AF:

0.224

AC:

1160

AN:

5170

South Asian (SAS)

AF:

0.396

AC:

1905

AN:

4816

European-Finnish (FIN)

AF:

0.477

AC:

5044

AN:

10564

Middle Eastern (MID)

AF:

0.395

AC:

116

AN:

294

European-Non Finnish (NFE)

AF:

0.460

AC:

31287

AN:

67980

Other (OTH)

AF:

0.373

AC:

787

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1693

3386

5079

6772

8465

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

534

1068

1602

2136

2670

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.427

Hom.:

18882

Bravo

AF:

0.350

Asia WGS

AF:

0.326

AC:

1131

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

8.1

(source)

DANN

Benign

0.91

PhyloP100

-0.88

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.080

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over