dbSNP rs11759141: ENSG00000287092:n.934-17820A>C (chr6-155850714-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000817237.1(ENSG00000287092):n.934-17820A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0658 in 152,222 control chromosomes in the GnomAD database, including 493 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 0.066 ( 493 hom., cov: 32)

Consequence

ENSG00000287092
ENST00000817237.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.689

Publications

1 publications found

Variant links:

Genes affected

ENSG00000287092 (HGNC:):

ENSG00000287092 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=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0998 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC101928923	XR_001744423.2 link	n.406-17820A>C	intron_variant	Intron 4 of 8
LOC105378072	XR_001744424.2 link	n.80-20660T>G	intron_variant	Intron 1 of 2
LOC105378072	XR_007059824.1 link	n.80-20660T>G	intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287092	ENST00000817237.1 link	n.934-17820A>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.0659

AC:

10018

AN:

152104

Hom.:

493

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0191

Gnomad AMI

AF:

0.146

Gnomad AMR

AF:

0.0774

Gnomad ASJ

AF:

0.0430

Gnomad EAS

AF:

0.000771

Gnomad SAS

AF:

0.0168

Gnomad FIN

AF:

0.0580

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.102

Gnomad OTH

AF:

0.0656

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

GnomAD4 genome

AF:

0.0658

AC:

10019

AN:

152222

Hom.:

493

Cov.:

AF XY:

0.0623

AC XY:

4634

AN XY:

74436

show subpopulations

African (AFR)

AF:

0.0191

AC:

793

AN:

41544

American (AMR)

AF:

0.0773

AC:

1181

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.0430

AC:

149

AN:

3468

East Asian (EAS)

AF:

0.000773

AC:

AN:

5176

South Asian (SAS)

AF:

0.0172

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.0580

AC:

616

AN:

10614

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.102

AC:

6922

AN:

68004

Other (OTH)

AF:

0.0649

AC:

137

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

469

938

1408

1877

2346

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

106

212

318

424

530

<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:

0.0890

Hom.:

1056

Bravo

AF:

0.0657

Asia WGS

AF:

0.0130

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

8.7

(source)

DANN

Benign

0.59

PhyloP100

0.69

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