dbSNP rs17111750: ENSG00000291038:n.915+141C>T (chr14-20442249-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 ENST00000687238.1(ENSG00000291038):n.915+141C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 151,978 control chromosomes in the GnomAD database, including 7,034 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 0.30 ( 7034 hom., cov: 32)

Consequence

ENSG00000291038
ENST00000687238.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00900

Publications

10 publications found

Variant links:

Genes affected

ENSG00000291038 (HGNC:):

ENSG00000291038 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=-0.99).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000291038	ENST00000687238.1 link	n.915+141C>T	intron_variant	Intron 6 of 7
ENSG00000291038	ENST00000700970.2 link	n.693+141C>T	intron_variant	Intron 4 of 4
ENSG00000291038	ENST00000800199.1 link	n.841+141C>T	intron_variant	Intron 6 of 7

Frequencies

GnomAD3 genomes

AF:

0.300

AC:

45536

AN:

151860

Hom.:

7029

Cov.:

show subpopulations

Gnomad AFR

AF:

0.277

Gnomad AMI

AF:

0.404

Gnomad AMR

AF:

0.242

Gnomad ASJ

AF:

0.405

Gnomad EAS

AF:

0.195

Gnomad SAS

AF:

0.375

Gnomad FIN

AF:

0.359

Gnomad MID

AF:

0.392

Gnomad NFE

AF:

0.312

Gnomad OTH

AF:

0.318

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

GnomAD4 genome

AF:

0.300

AC:

45570

AN:

151978

Hom.:

7034

Cov.:

AF XY:

0.302

AC XY:

22423

AN XY:

74264

show subpopulations

African (AFR)

AF:

0.278

AC:

11507

AN:

41450

American (AMR)

AF:

0.242

AC:

3694

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.405

AC:

1406

AN:

3472

East Asian (EAS)

AF:

0.195

AC:

1009

AN:

5166

South Asian (SAS)

AF:

0.374

AC:

1803

AN:

4816

European-Finnish (FIN)

AF:

0.359

AC:

3779

AN:

10528

Middle Eastern (MID)

AF:

0.374

AC:

110

AN:

294

European-Non Finnish (NFE)

AF:

0.312

AC:

21222

AN:

67962

Other (OTH)

AF:

0.319

AC:

672

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1646

3292

4938

6584

8230

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

476

952

1428

1904

2380

<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:

0.305

Hom.:

12224

Bravo

AF:

0.289

Asia WGS

AF:

0.306

AC:

1064

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.6

(source)

DANN

Benign

0.64

PhyloP100

0.0090

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