dbSNP rs17259784: ENSG00000310018:n.139-29173G>C (chr1-208584241-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000846586.1(ENSG00000310018):n.139-29173G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,206 control chromosomes in the GnomAD database, including 1,488 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 ( 1488 hom., cov: 32)

Consequence

ENSG00000310018
ENST00000846586.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.554

Publications

13 publications found

Variant links:

COSMIC-nc: COSV60020952

Genes affected

ENSG00000310018 (HGNC:):

ENSG00000310018 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=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000310018	ENST00000846586.1 link	n.139-29173G>C	intron_variant	Intron 1 of 2
ENSG00000310018	ENST00000846587.1 link	n.119-29173G>C	intron_variant	Intron 1 of 1
ENSG00000310018	ENST00000846588.1 link	n.119-23115G>C	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.125

AC:

18994

AN:

152088

Hom.:

1493

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0486

Gnomad AMI

AF:

0.266

Gnomad AMR

AF:

0.104

Gnomad ASJ

AF:

0.148

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.153

Gnomad FIN

AF:

0.171

Gnomad MID

AF:

0.209

Gnomad NFE

AF:

0.173

Gnomad OTH

AF:

0.122

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

GnomAD4 genome

AF:

0.125

AC:

18989

AN:

152206

Hom.:

1488

Cov.:

AF XY:

0.124

AC XY:

9264

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.0486

AC:

2022

AN:

41566

American (AMR)

AF:

0.104

AC:

1593

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.148

AC:

514

AN:

3464

East Asian (EAS)

AF:

0.00135

AC:

AN:

5186

South Asian (SAS)

AF:

0.152

AC:

735

AN:

4820

European-Finnish (FIN)

AF:

0.171

AC:

1808

AN:

10586

Middle Eastern (MID)

AF:

0.197

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.173

AC:

11760

AN:

67988

Other (OTH)

AF:

0.120

AC:

253

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

841

1682

2523

3364

4205

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

212

424

636

848

1060

<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:

0.158

Hom.:

1125

Bravo

AF:

0.114

Asia WGS

AF:

0.0740

AC:

260

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

4.6

(source)

DANN

Benign

0.65

PhyloP100

-0.55

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