Genetic Variant ENSG00000254367:n.625-8365C>T (chr8-8732099-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 ENST00000522213.5(ENSG00000254367):n.625-8365C>T 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 152,140 control chromosomes in the GnomAD database, including 1,583 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 ( 1583 hom., cov: 32)

Consequence

ENSG00000254367
ENST00000522213.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.620

Publications

4 publications found

Variant links:

Genes affected

ENSG00000254367 (HGNC:):

ENSG00000254367 links:

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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 (NFE) allele frequency at 95% confidence interval = 0.178 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.625-8365C>T	intron_variant	Intron 3 of 3	2
ENSG00000254367	ENST00000765578.1 link	n.456-8365C>T	intron_variant	Intron 2 of 3
ENSG00000254367	ENST00000765579.1 link	n.407-7060C>T	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.123

AC:

18763

AN:

152022

Hom.:

1583

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0323

Gnomad AMI

AF:

0.104

Gnomad AMR

AF:

0.0889

Gnomad ASJ

AF:

0.167

Gnomad EAS

AF:

0.0467

Gnomad SAS

AF:

0.152

Gnomad FIN

AF:

0.173

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.180

Gnomad OTH

AF:

0.139

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

GnomAD4 genome

AF:

0.123

AC:

18764

AN:

152140

Hom.:

1583

Cov.:

AF XY:

0.123

AC XY:

9175

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.0322

AC:

1338

AN:

41522

American (AMR)

AF:

0.0888

AC:

1357

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.167

AC:

581

AN:

3470

East Asian (EAS)

AF:

0.0467

AC:

241

AN:

5166

South Asian (SAS)

AF:

0.152

AC:

732

AN:

4816

European-Finnish (FIN)

AF:

0.173

AC:

1830

AN:

10582

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.180

AC:

12266

AN:

67984

Other (OTH)

AF:

0.136

AC:

287

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

802

1604

2407

3209

4011

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

218

436

654

872

1090

<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:

0.0988

Hom.:

212

Bravo

AF:

0.110

Asia WGS

AF:

0.0870

AC:

303

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

4.0

(source)

DANN

Benign

0.62

PhyloP100

0.62

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