dbSNP rs12555508: ENSG00000285634:n.181-3594C>T (chr9-85406281-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 ENST00000648131.1(ENSG00000285634):n.181-3594C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,232 control chromosomes in the GnomAD database, including 1,173 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 0.11 ( 1173 hom., cov: 33)

Consequence

ENSG00000285634
ENST00000648131.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.525

Publications

1 publications found

Variant links:

Genes affected

ENSG00000285634 (HGNC:):

ENSG00000285634 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=-0.95).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376121	XR_001746810.2 link	n.312-3594C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000285634	ENST00000648131.1 link	n.181-3594C>T	intron_variant	Intron 1 of 3
ENSG00000285634	ENST00000661197.3 link	n.780-3594C>T	intron_variant	Intron 1 of 1
ENSG00000285634	ENST00000662737.1 link	n.448-3594C>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.105

AC:

15970

AN:

152114

Hom.:

1159

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0259

Gnomad AMI

AF:

0.0855

Gnomad AMR

AF:

0.223

Gnomad ASJ

AF:

0.144

Gnomad EAS

AF:

0.0534

Gnomad SAS

AF:

0.103

Gnomad FIN

AF:

0.160

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.120

Gnomad OTH

AF:

0.107

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

GnomAD4 genome

AF:

0.105

AC:

15990

AN:

152232

Hom.:

1173

Cov.:

AF XY:

0.109

AC XY:

8078

AN XY:

74434

show subpopulations

African (AFR)

AF:

0.0258

AC:

1073

AN:

41556

American (AMR)

AF:

0.224

AC:

3433

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.144

AC:

499

AN:

3472

East Asian (EAS)

AF:

0.0532

AC:

275

AN:

5174

South Asian (SAS)

AF:

0.102

AC:

490

AN:

4822

European-Finnish (FIN)

AF:

0.160

AC:

1692

AN:

10582

Middle Eastern (MID)

AF:

0.122

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.120

AC:

8192

AN:

68010

Other (OTH)

AF:

0.105

AC:

222

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

723

1447

2170

2894

3617

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

178

356

534

712

890

<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:

0.120

Hom.:

232

Bravo

AF:

0.108

Asia WGS

AF:

0.0800

AC:

277

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.33

(source)

DANN

Benign

0.64

PhyloP100

-0.53

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