dbSNP rs2145231: ENSG00000286117:n.120+7400G>A (chr20-23644910-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 ENST00000801340.1(ENSG00000286117):n.120+7400G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,032 control chromosomes in the GnomAD database, including 3,256 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 0.20 ( 3256 hom., cov: 32)

Consequence

ENSG00000286117
ENST00000801340.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.22

Publications

14 publications found

Variant links:

Genes affected

ENSG00000286117 (HGNC:):

ENSG00000286117 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=-0.87).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286117	ENST00000801340.1 link	n.120+7400G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.195

AC:

29633

AN:

151914

Hom.:

3253

Cov.:

show subpopulations

Gnomad AFR

AF:

0.286

Gnomad AMI

AF:

0.0570

Gnomad AMR

AF:

0.116

Gnomad ASJ

AF:

0.127

Gnomad EAS

AF:

0.0931

Gnomad SAS

AF:

0.293

Gnomad FIN

AF:

0.191

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.165

Gnomad OTH

AF:

0.176

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

GnomAD4 genome

AF:

0.195

AC:

29651

AN:

152032

Hom.:

3256

Cov.:

AF XY:

0.196

AC XY:

14530

AN XY:

74300

show subpopulations

African (AFR)

AF:

0.285

AC:

11826

AN:

41424

American (AMR)

AF:

0.116

AC:

1776

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.127

AC:

441

AN:

3470

East Asian (EAS)

AF:

0.0929

AC:

481

AN:

5178

South Asian (SAS)

AF:

0.292

AC:

1407

AN:

4816

European-Finnish (FIN)

AF:

0.191

AC:

2017

AN:

10570

Middle Eastern (MID)

AF:

0.153

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.165

AC:

11242

AN:

67986

Other (OTH)

AF:

0.173

AC:

364

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1203

2406

3610

4813

6016

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

324

648

972

1296

1620

<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:

0.170

Hom.:

2482

Bravo

AF:

0.188

Asia WGS

AF:

0.173

AC:

603

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.85

(source)

DANN

Benign

0.95

PhyloP100

-1.2

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