dbSNP rs17500692: ENSG00000265179:n.179-6093C>T (chr18-900788-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000582554.2(ENSG00000265179):n.179-6093C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,136 control chromosomes in the GnomAD database, including 1,766 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 ( 1766 hom., cov: 33)

Consequence

ENSG00000265179
ENST00000582554.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.02

Publications

2 publications found

Variant links:

Genes affected

ENSG00000265179 (HGNC:):

ENSG00000265179 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000265179	ENST00000582554.2 link	n.179-6093C>T	intron_variant	Intron 1 of 1	5
ENSG00000265179	ENST00000717225.1 link	n.261+4675C>T	intron_variant	Intron 1 of 1
ENSG00000265179	ENST00000717226.1 link	n.340+3361C>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.146

AC:

22175

AN:

152018

Hom.:

1758

Cov.:

show subpopulations

Gnomad AFR

AF:

0.181

Gnomad AMI

AF:

0.260

Gnomad AMR

AF:

0.0851

Gnomad ASJ

AF:

0.143

Gnomad EAS

AF:

0.236

Gnomad SAS

AF:

0.198

Gnomad FIN

AF:

0.112

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.131

Gnomad OTH

AF:

0.150

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

GnomAD4 genome

AF:

0.146

AC:

22227

AN:

152136

Hom.:

1766

Cov.:

AF XY:

0.145

AC XY:

10781

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.181

AC:

7522

AN:

41478

American (AMR)

AF:

0.0850

AC:

1299

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.143

AC:

495

AN:

3470

East Asian (EAS)

AF:

0.236

AC:

1224

AN:

5180

South Asian (SAS)

AF:

0.199

AC:

960

AN:

4816

European-Finnish (FIN)

AF:

0.112

AC:

1186

AN:

10578

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.131

AC:

8939

AN:

68018

Other (OTH)

AF:

0.154

AC:

325

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

983

1967

2950

3934

4917

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

248

496

744

992

1240

<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:

0.134

Hom.:

6398

Bravo

AF:

0.143

Asia WGS

AF:

0.236

AC:

822

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.048

(source)

DANN

Benign

0.63

PhyloP100

-1.0

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