dbSNP rs554241: ENSG00000254367:n.625-14368G>A (chr8-8738102-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 ENST00000522213.5(ENSG00000254367):n.625-14368G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,030 control chromosomes in the GnomAD database, including 2,562 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 0.17 ( 2562 hom., cov: 32)

Consequence

ENSG00000254367
ENST00000522213.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.240

Publications

1 publications found

Variant links:

Genes affected

ENSG00000254367 (HGNC:):

ENSG00000254367 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.292 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
ENSG00000254367	ENST00000522213.5 link	n.625-14368G>A	intron_variant	Intron 3 of 3	2
ENSG00000254367	ENST00000765578.1 link	n.456-14368G>A	intron_variant	Intron 2 of 3
ENSG00000254367	ENST00000765579.1 link	n.407-13063G>A	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.165

AC:

25096

AN:

151914

Hom.:

2557

Cov.:

show subpopulations

Gnomad AFR

AF:

0.297

Gnomad AMI

AF:

0.0758

Gnomad AMR

AF:

0.120

Gnomad ASJ

AF:

0.130

Gnomad EAS

AF:

0.110

Gnomad SAS

AF:

0.102

Gnomad FIN

AF:

0.140

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.111

Gnomad OTH

AF:

0.160

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

GnomAD4 genome

AF:

0.165

AC:

25113

AN:

152030

Hom.:

2562

Cov.:

AF XY:

0.163

AC XY:

12133

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.296

AC:

12283

AN:

41430

American (AMR)

AF:

0.120

AC:

1830

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.130

AC:

452

AN:

3470

East Asian (EAS)

AF:

0.110

AC:

571

AN:

5170

South Asian (SAS)

AF:

0.101

AC:

486

AN:

4808

European-Finnish (FIN)

AF:

0.140

AC:

1478

AN:

10568

Middle Eastern (MID)

AF:

0.224

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.111

AC:

7541

AN:

67996

Other (OTH)

AF:

0.160

AC:

337

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1018

2035

3053

4070

5088

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

270

540

810

1080

1350

<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:

0.123

Hom.:

742

Bravo

AF:

0.169

Asia WGS

AF:

0.128

AC:

445

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.43

(source)

DANN

Benign

0.19

PhyloP100

-0.24

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