dbSNP rs156331: ENSG00000286288:n.951-35118G>T (chr20-1846342-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000716594.1(ENSG00000286288):n.951-35118G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,184 control chromosomes in the GnomAD database, including 5,411 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 0.25 ( 5411 hom., cov: 33)

Consequence

ENSG00000286288
ENST00000716594.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.38

Publications

7 publications found

Variant links:

Genes affected

ENSG00000286288 (HGNC:):

ENSG00000286288 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=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000286288	ENST00000716594.1 link	n.951-35118G>T	intron_variant	Intron 2 of 5
ENSG00000286288	ENST00000844949.1 link	n.102+28673G>T	intron_variant	Intron 1 of 2
ENSG00000286288	ENST00000844950.1 link	n.120+15425G>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.255

AC:

38748

AN:

152066

Hom.:

5403

Cov.:

show subpopulations

Gnomad AFR

AF:

0.352

Gnomad AMI

AF:

0.173

Gnomad AMR

AF:

0.206

Gnomad ASJ

AF:

0.378

Gnomad EAS

AF:

0.410

Gnomad SAS

AF:

0.221

Gnomad FIN

AF:

0.238

Gnomad MID

AF:

0.420

Gnomad NFE

AF:

0.193

Gnomad OTH

AF:

0.270

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

GnomAD4 genome

AF:

0.255

AC:

38789

AN:

152184

Hom.:

5411

Cov.:

AF XY:

0.255

AC XY:

19006

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.352

AC:

14621

AN:

41494

American (AMR)

AF:

0.206

AC:

3148

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.378

AC:

1313

AN:

3472

East Asian (EAS)

AF:

0.410

AC:

2123

AN:

5176

South Asian (SAS)

AF:

0.221

AC:

1067

AN:

4820

European-Finnish (FIN)

AF:

0.238

AC:

2519

AN:

10598

Middle Eastern (MID)

AF:

0.432

AC:

126

AN:

292

European-Non Finnish (NFE)

AF:

0.193

AC:

13145

AN:

68018

Other (OTH)

AF:

0.269

AC:

570

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1477

2954

4431

5908

7385

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

398

796

1194

1592

1990

<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:

0.211

Hom.:

6264

Bravo

AF:

0.259

Asia WGS

AF:

0.288

AC:

998

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.0

(source)

DANN

Benign

0.62

PhyloP100

-2.4

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over