dbSNP rs1883701: ENSG00000286972:n.324-3882G>A (chr20-40753199-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000655799.1(ENSG00000286972):n.324-3882G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0173 in 152,232 control chromosomes in the GnomAD database, including 186 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 0.017 ( 186 hom., cov: 32)

Consequence

ENSG00000286972
ENST00000655799.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.439

Publications

1 publications found

Variant links:

Genes affected

ENSG00000286972 (HGNC:):

ENSG00000286972 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000286972	ENST00000655799.1 link	n.324-3882G>A	intron_variant	Intron 1 of 1
ENSG00000229771	ENST00000758964.1 link	n.168+24863C>T	intron_variant	Intron 2 of 5
ENSG00000298935	ENST00000759166.1 link	n.75+4007C>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0173

AC:

2630

AN:

152112

Hom.:

185

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00215

Gnomad AMI

AF:

0.0692

Gnomad AMR

AF:

0.0123

Gnomad ASJ

AF:

0.0135

Gnomad EAS

AF:

0.264

Gnomad SAS

AF:

0.0464

Gnomad FIN

AF:

0.00698

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00791

Gnomad OTH

AF:

0.0163

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

GnomAD4 genome

AF:

0.0173

AC:

2632

AN:

152232

Hom.:

186

Cov.:

AF XY:

0.0191

AC XY:

1425

AN XY:

74414

show subpopulations

African (AFR)

AF:

0.00214

AC:

AN:

41564

American (AMR)

AF:

0.0127

AC:

194

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.0135

AC:

AN:

3472

East Asian (EAS)

AF:

0.264

AC:

1365

AN:

5168

South Asian (SAS)

AF:

0.0465

AC:

224

AN:

4820

European-Finnish (FIN)

AF:

0.00698

AC:

AN:

10604

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00791

AC:

538

AN:

68022

Other (OTH)

AF:

0.0161

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

120

240

361

481

601

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

126

168

210

<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:

0.00855

Hom.:

Bravo

AF:

0.0182

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.0

(source)

DANN

Benign

0.67

PhyloP100

0.44

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over