dbSNP rs2464: MAVS:c.*8188C>T (chr20-3874335-C-T) – 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.*8188C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 397,218 control chromosomes in the GnomAD database, including 33,943 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 ( 11172 hom., cov: 31)

Exomes 𝑓: 0.42 ( 22771 hom. )

Consequence

MAVS
NM_020746.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0390

Publications

12 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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
MAVS	NM_020746.5 link	c.*8188C>T	3_prime_UTR_variant	Exon 7 of 7	ENST00000428216.4	NP_065797.2	Q7Z434-1
MAVS	NR_037921.2 link	n.9775C>T	non_coding_transcript_exon_variant	Exon 6 of 6
MAVS	NM_001206491.2 link	c.*8188C>T	3_prime_UTR_variant	Exon 6 of 6		NP_001193420.1	Q7Z434-4
MAVS	NM_001385663.1 link	c.*8188C>T	3_prime_UTR_variant	Exon 8 of 8		NP_001372592.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
MAVS	ENST00000428216.4 link	c.*8188C>T	3_prime_UTR_variant	Exon 7 of 7	1	NM_020746.5	ENSP00000401980.2	Q7Z434-1
MAVS	ENST00000416600.6 link	c.*8188C>T	3_prime_UTR_variant	Exon 6 of 6	1		ENSP00000413749.2	Q7Z434-4
PANK2-AS1	ENST00000725519.1 link	n.516G>A	non_coding_transcript_exon_variant	Exon 2 of 2
PANK2-AS1	ENST00000725518.1 link	n.426-11445G>A	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.360

AC:

54690

AN:

151734

Hom.:

11169

Cov.:

show subpopulations

Gnomad AFR

AF:

0.159

Gnomad AMI

AF:

0.547

Gnomad AMR

AF:

0.405

Gnomad ASJ

AF:

0.374

Gnomad EAS

AF:

0.217

Gnomad SAS

AF:

0.389

Gnomad FIN

AF:

0.480

Gnomad MID

AF:

0.386

Gnomad NFE

AF:

0.460

Gnomad OTH

AF:

0.370

GnomAD4 exome

AF:

0.421

AC:

103420

AN:

245366

Hom.:

22771

Cov.:

AF XY:

0.423

AC XY:

52637

AN XY:

124346

show subpopulations

African (AFR)

AF:

0.165

AC:

1183

AN:

7172

American (AMR)

AF:

0.422

AC:

3133

AN:

7432

Ashkenazi Jewish (ASJ)

AF:

0.362

AC:

3335

AN:

9224

East Asian (EAS)

AF:

0.225

AC:

5146

AN:

22856

South Asian (SAS)

AF:

0.367

AC:

890

AN:

2422

European-Finnish (FIN)

AF:

0.465

AC:

9677

AN:

20822

Middle Eastern (MID)

AF:

0.378

AC:

489

AN:

1294

European-Non Finnish (NFE)

AF:

0.463

AC:

73092

AN:

157814

Other (OTH)

AF:

0.397

AC:

6475

AN:

16330

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

3042

6084

9126

12168

15210

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

282

564

846

1128

1410

<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:

0.360

AC:

54698

AN:

151852

Hom.:

11172

Cov.:

AF XY:

0.361

AC XY:

26782

AN XY:

74190

show subpopulations

African (AFR)

AF:

0.159

AC:

6579

AN:

41402

American (AMR)

AF:

0.406

AC:

6188

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.374

AC:

1299

AN:

3470

East Asian (EAS)

AF:

0.215

AC:

1112

AN:

5162

South Asian (SAS)

AF:

0.390

AC:

1873

AN:

4806

European-Finnish (FIN)

AF:

0.480

AC:

5044

AN:

10518

Middle Eastern (MID)

AF:

0.371

AC:

109

AN:

294

European-Non Finnish (NFE)

AF:

0.460

AC:

31215

AN:

67920

Other (OTH)

AF:

0.369

AC:

780

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1665

3330

4996

6661

8326

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

532

1064

1596

2128

2660

<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:

0.383

Hom.:

2357

Bravo

AF:

0.348

Asia WGS

AF:

0.316

AC:

1099

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

1.1

(source)

DANN

Benign

0.63

PhyloP100

0.039

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over