dbSNP rs10507450: ENSG00000307651:n.233-15680A>T (chr13-37291672-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000827668.1(ENSG00000307651):n.233-15680A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.08 in 152,246 control chromosomes in the GnomAD database, including 641 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 0.080 ( 641 hom., cov: 33)

Consequence

ENSG00000307651
ENST00000827668.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.177

Publications

0 publications found

Variant links:

Genes affected

ENSG00000307651 (HGNC:):

ENSG00000307651 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=-0.9).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.118 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
ENSG00000307651	ENST00000827668.1 link	n.233-15680A>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0800

AC:

12171

AN:

152128

Hom.:

637

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0342

Gnomad AMI

AF:

0.0329

Gnomad AMR

AF:

0.122

Gnomad ASJ

AF:

0.143

Gnomad EAS

AF:

0.00173

Gnomad SAS

AF:

0.0996

Gnomad FIN

AF:

0.0648

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.102

Gnomad OTH

AF:

0.0928

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

GnomAD4 genome

AF:

0.0800

AC:

12181

AN:

152246

Hom.:

641

Cov.:

AF XY:

0.0789

AC XY:

5875

AN XY:

74444

show subpopulations

African (AFR)

AF:

0.0342

AC:

1420

AN:

41570

American (AMR)

AF:

0.123

AC:

1878

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.143

AC:

496

AN:

3472

East Asian (EAS)

AF:

0.00174

AC:

AN:

5180

South Asian (SAS)

AF:

0.100

AC:

484

AN:

4834

European-Finnish (FIN)

AF:

0.0648

AC:

687

AN:

10606

Middle Eastern (MID)

AF:

0.122

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.102

AC:

6946

AN:

67980

Other (OTH)

AF:

0.0923

AC:

195

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

575

1150

1726

2301

2876

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

142

284

426

568

710

<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:

0.0879

Hom.:

Bravo

AF:

0.0843

Asia WGS

AF:

0.0410

AC:

143

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

6.0

(source)

DANN

Benign

0.61

PhyloP100

0.18

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