dbSNP rs9906155: ENSG00000267506:n.126-23987T>C (chr17-77705615-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 ENST00000715849.1(ENSG00000267506):n.126-23987T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0488 in 152,044 control chromosomes in the GnomAD database, including 221 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 0.049 ( 221 hom., cov: 32)

Consequence

ENSG00000267506
ENST00000715849.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.703

Publications

9 publications found

Variant links:

Genes affected

ENSG00000267506 (HGNC:58772):

ENSG00000267506 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 (AFR) allele frequency at 95% confidence interval = 0.0614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000267506	ENST00000715849.1 link	n.126-23987T>C	intron_variant	Intron 2 of 3
ENSG00000267506	ENST00000715851.1 link	n.585-1418T>C	intron_variant	Intron 2 of 2
ENSG00000267506	ENST00000715858.1 link	n.70+20251T>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0487

AC:

7403

AN:

151928

Hom.:

217

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0631

Gnomad AMI

AF:

0.0340

Gnomad AMR

AF:

0.0301

Gnomad ASJ

AF:

0.0360

Gnomad EAS

AF:

0.0527

Gnomad SAS

AF:

0.0432

Gnomad FIN

AF:

0.0165

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0506

Gnomad OTH

AF:

0.0373

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

GnomAD4 genome

AF:

0.0488

AC:

7425

AN:

152044

Hom.:

221

Cov.:

AF XY:

0.0469

AC XY:

3484

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.0634

AC:

2630

AN:

41464

American (AMR)

AF:

0.0300

AC:

459

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0360

AC:

125

AN:

3470

East Asian (EAS)

AF:

0.0526

AC:

272

AN:

5168

South Asian (SAS)

AF:

0.0428

AC:

206

AN:

4812

European-Finnish (FIN)

AF:

0.0165

AC:

174

AN:

10544

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0506

AC:

3442

AN:

67986

Other (OTH)

AF:

0.0388

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

350

700

1051

1401

1751

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

184

276

368

460

<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:

0.0504

Hom.:

Bravo

AF:

0.0501

Asia WGS

AF:

0.0460

AC:

163

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

1.6

(source)

DANN

Benign

0.49

PhyloP100

-0.70

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