dbSNP rs11047543: ENSG00000296761:n.372-17595C>T (chr12-24635405-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 ENST00000741714.1(ENSG00000296761):n.372-17595C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 151,788 control chromosomes in the GnomAD database, including 1,307 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 0.12 ( 1307 hom., cov: 32)

Consequence

ENSG00000296761
ENST00000741714.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0130

Publications

43 publications found

Variant links:

Genes affected

ENSG00000296761 (HGNC:):

ENSG00000296761 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=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369698	XR_001749046.2 link	n.327-17595C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296761	ENST00000741714.1 link	n.372-17595C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.120

AC:

18172

AN:

151670

Hom.:

1305

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0407

Gnomad AMI

AF:

0.128

Gnomad AMR

AF:

0.162

Gnomad ASJ

AF:

0.167

Gnomad EAS

AF:

0.129

Gnomad SAS

AF:

0.255

Gnomad FIN

AF:

0.105

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.147

Gnomad OTH

AF:

0.147

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

GnomAD4 genome

AF:

0.120

AC:

18181

AN:

151788

Hom.:

1307

Cov.:

AF XY:

0.120

AC XY:

8936

AN XY:

74200

show subpopulations

African (AFR)

AF:

0.0406

AC:

1683

AN:

41464

American (AMR)

AF:

0.163

AC:

2473

AN:

15212

Ashkenazi Jewish (ASJ)

AF:

0.167

AC:

578

AN:

3462

East Asian (EAS)

AF:

0.128

AC:

660

AN:

5160

South Asian (SAS)

AF:

0.256

AC:

1231

AN:

4810

European-Finnish (FIN)

AF:

0.105

AC:

1109

AN:

10588

Middle Eastern (MID)

AF:

0.180

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.147

AC:

9965

AN:

67780

Other (OTH)

AF:

0.148

AC:

312

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

813

1627

2440

3254

4067

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

208

416

624

832

1040

<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:

0.142

Hom.:

4765

Bravo

AF:

0.120

Asia WGS

AF:

0.191

AC:

662

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.4

(source)

DANN

Benign

0.77

PhyloP100

0.013

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