dbSNP rs1524846: ENSG00000286973:n.509+23150A>C (chr15-23780723-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000658937.2(ENSG00000286973):n.509+23150A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0553 in 152,340 control chromosomes in the GnomAD database, including 522 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 0.055 ( 522 hom., cov: 32)

Consequence

ENSG00000286973
ENST00000658937.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.237

Publications

1 publications found

Variant links:

Genes affected

ENSG00000286973 (HGNC:):

ENSG00000286973 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 (AFR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000286973	ENST00000658937.2 link	n.509+23150A>C	intron_variant	Intron 1 of 2
ENSG00000286973	ENST00000844005.1 link	n.600+8943A>C	intron_variant	Intron 2 of 3
ENSG00000286973	ENST00000844006.1 link	n.471+23150A>C	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.0553

AC:

8413

AN:

152222

Hom.:

519

Cov.:

show subpopulations

Gnomad AFR

AF:

0.154

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0246

Gnomad ASJ

AF:

0.0104

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.0685

Gnomad FIN

AF:

0.0104

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0158

Gnomad OTH

AF:

0.0388

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

GnomAD4 genome

AF:

0.0553

AC:

8420

AN:

152340

Hom.:

522

Cov.:

AF XY:

0.0541

AC XY:

4034

AN XY:

74506

show subpopulations

African (AFR)

AF:

0.154

AC:

6404

AN:

41558

American (AMR)

AF:

0.0245

AC:

375

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.0104

AC:

AN:

3472

East Asian (EAS)

AF:

0.000578

AC:

AN:

5186

South Asian (SAS)

AF:

0.0681

AC:

329

AN:

4828

European-Finnish (FIN)

AF:

0.0104

AC:

111

AN:

10628

Middle Eastern (MID)

AF:

0.0238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0158

AC:

1072

AN:

68042

Other (OTH)

AF:

0.0393

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

382

765

1147

1530

1912

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

264

352

440

<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:

0.0376

Hom.:

412

Bravo

AF:

0.0598

Asia WGS

AF:

0.0570

AC:

199

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

0.86

(source)

DANN

Benign

0.65

PhyloP100

-0.24

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