dbSNP rs12913838: ENSG00000306185:n.65+7012T>C (chr15-87813028-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000816143.1(ENSG00000306185):n.65+7012T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 151,938 control chromosomes in the GnomAD database, including 7,223 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 0.29 ( 7223 hom., cov: 33)

Consequence

ENSG00000306185
ENST00000816143.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.373

Publications

1 publications found

Variant links:

Genes affected

ENSG00000306185 (HGNC:):

ENSG00000306185 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=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306185	ENST00000816143.1 link	n.65+7012T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.294

AC:

44564

AN:

151822

Hom.:

7225

Cov.:

show subpopulations

Gnomad AFR

AF:

0.147

Gnomad AMI

AF:

0.365

Gnomad AMR

AF:

0.374

Gnomad ASJ

AF:

0.368

Gnomad EAS

AF:

0.401

Gnomad SAS

AF:

0.343

Gnomad FIN

AF:

0.295

Gnomad MID

AF:

0.360

Gnomad NFE

AF:

0.347

Gnomad OTH

AF:

0.315

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

GnomAD4 genome

AF:

0.293

AC:

44560

AN:

151938

Hom.:

7223

Cov.:

AF XY:

0.295

AC XY:

21894

AN XY:

74238

show subpopulations

African (AFR)

AF:

0.147

AC:

6081

AN:

41494

American (AMR)

AF:

0.374

AC:

5710

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.368

AC:

1275

AN:

3468

East Asian (EAS)

AF:

0.401

AC:

2060

AN:

5140

South Asian (SAS)

AF:

0.343

AC:

1652

AN:

4822

European-Finnish (FIN)

AF:

0.295

AC:

3103

AN:

10536

Middle Eastern (MID)

AF:

0.355

AC:

103

AN:

290

European-Non Finnish (NFE)

AF:

0.347

AC:

23581

AN:

67918

Other (OTH)

AF:

0.314

AC:

663

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1598

3197

4795

6394

7992

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

458

916

1374

1832

2290

<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:

0.232

Hom.:

1818

Bravo

AF:

0.291

Asia WGS

AF:

0.363

AC:

1260

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

4.7

(source)

DANN

Benign

0.63

PhyloP100

0.37

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