dbSNP rs10500777: ENSG00000302524:n.65+2813C>T (chr11-13254764-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000787640.1(ENSG00000302524):n.65+2813C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,090 control chromosomes in the GnomAD database, including 1,923 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 0.15 ( 1923 hom., cov: 33)

Consequence

ENSG00000302524
ENST00000787640.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.487

Publications

1 publications found

Variant links:

Genes affected

ENSG00000302524 (HGNC:):

ENSG00000302524 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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.213 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
ENSG00000302524	ENST00000787640.1 link	n.65+2813C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.154

AC:

23371

AN:

151972

Hom.:

1919

Cov.:

show subpopulations

Gnomad AFR

AF:

0.140

Gnomad AMI

AF:

0.245

Gnomad AMR

AF:

0.151

Gnomad ASJ

AF:

0.183

Gnomad EAS

AF:

0.223

Gnomad SAS

AF:

0.196

Gnomad FIN

AF:

0.205

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.144

Gnomad OTH

AF:

0.153

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

GnomAD4 genome

AF:

0.154

AC:

23392

AN:

152090

Hom.:

1923

Cov.:

AF XY:

0.159

AC XY:

11789

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.140

AC:

5815

AN:

41476

American (AMR)

AF:

0.151

AC:

2308

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.183

AC:

636

AN:

3470

East Asian (EAS)

AF:

0.223

AC:

1154

AN:

5168

South Asian (SAS)

AF:

0.198

AC:

953

AN:

4818

European-Finnish (FIN)

AF:

0.205

AC:

2169

AN:

10574

Middle Eastern (MID)

AF:

0.163

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.144

AC:

9764

AN:

67990

Other (OTH)

AF:

0.153

AC:

322

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1015

2030

3044

4059

5074

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

262

524

786

1048

1310

<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:

0.148

Hom.:

216

Bravo

AF:

0.151

Asia WGS

AF:

0.201

AC:

698

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

3.7

(source)

DANN

Benign

0.67

PhyloP100

-0.49

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