dbSNP rs10518854: ENSG00000293736:n.258+8296T>C (chr15-56527966-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000718648.1(ENSG00000293736):n.258+8296T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,210 control chromosomes in the GnomAD database, including 1,153 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 0.12 ( 1153 hom., cov: 32)

Consequence

ENSG00000293736
ENST00000718648.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.908

Publications

1 publications found

Variant links:

Genes affected

ENSG00000293736 (HGNC:):

ENSG00000293736 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=-0.81).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370832	XR_007064652.1 link	n.222-30893T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293736	ENST00000718648.1 link	n.258+8296T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.123

AC:

18740

AN:

152090

Hom.:

1156

Cov.:

show subpopulations

Gnomad AFR

AF:

0.130

Gnomad AMI

AF:

0.0681

Gnomad AMR

AF:

0.137

Gnomad ASJ

AF:

0.113

Gnomad EAS

AF:

0.155

Gnomad SAS

AF:

0.191

Gnomad FIN

AF:

0.147

Gnomad MID

AF:

0.204

Gnomad NFE

AF:

0.105

Gnomad OTH

AF:

0.133

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

GnomAD4 genome

AF:

0.123

AC:

18758

AN:

152210

Hom.:

1153

Cov.:

AF XY:

0.129

AC XY:

9568

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.131

AC:

5429

AN:

41532

American (AMR)

AF:

0.137

AC:

2097

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.113

AC:

394

AN:

3472

East Asian (EAS)

AF:

0.154

AC:

796

AN:

5172

South Asian (SAS)

AF:

0.190

AC:

917

AN:

4818

European-Finnish (FIN)

AF:

0.147

AC:

1562

AN:

10600

Middle Eastern (MID)

AF:

0.211

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.105

AC:

7161

AN:

68006

Other (OTH)

AF:

0.132

AC:

278

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

863

1726

2590

3453

4316

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

220

440

660

880

1100

<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:

0.110

Hom.:

1457

Bravo

AF:

0.119

Asia WGS

AF:

0.140

AC:

486

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

6.3

(source)

DANN

Benign

0.56

PhyloP100

0.91

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