Genetic Variant ENSG00000253363:n.517-31601A>G (chr8-36527313-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 ENST00000651399.1(ENSG00000253363):n.517-31601A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 151,926 control chromosomes in the GnomAD database, including 3,306 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 0.18 ( 3306 hom., cov: 32)

Consequence

ENSG00000253363
ENST00000651399.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0640

Publications

3 publications found

Variant links:

Genes affected

ENSG00000253363 (HGNC:):

ENSG00000253363 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253363	ENST00000651399.1 link	n.517-31601A>G		intron_variant	Intron 4 of 5
ENSG00000253363	ENST00000656455.2 link	n.485-100249A>G		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes

AF:

0.178

AC:

27049

AN:

151808

Hom.:

3293

Cov.:

show subpopulations

Gnomad AFR

AF:

0.339

Gnomad AMI

AF:

0.0110

Gnomad AMR

AF:

0.133

Gnomad ASJ

AF:

0.129

Gnomad EAS

AF:

0.281

Gnomad SAS

AF:

0.211

Gnomad FIN

AF:

0.101

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.0974

Gnomad OTH

AF:

0.179

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

GnomAD4 genome

AF:

0.178

AC:

27109

AN:

151926

Hom.:

3306

Cov.:

AF XY:

0.180

AC XY:

13355

AN XY:

74262

show subpopulations

African (AFR)

AF:

0.339

AC:

14048

AN:

41408

American (AMR)

AF:

0.133

AC:

2027

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.129

AC:

446

AN:

3470

East Asian (EAS)

AF:

0.281

AC:

1442

AN:

5132

South Asian (SAS)

AF:

0.211

AC:

1019

AN:

4828

European-Finnish (FIN)

AF:

0.101

AC:

1071

AN:

10592

Middle Eastern (MID)

AF:

0.184

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0974

AC:

6614

AN:

67934

Other (OTH)

AF:

0.179

AC:

378

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1050

2100

3149

4199

5249

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

280

560

840

1120

1400

<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:

0.122

Hom.:

796

Bravo

AF:

0.186

Asia WGS

AF:

0.278

AC:

962

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

4.7

(source)

DANN

Benign

0.50

PhyloP100

0.064

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