Genetic Variant ENST00000657734.1:n.1326+32485C>G (chr8-21262649-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 ENST00000657734.1(ENSG00000254092):n.1326+32485C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0507 in 152,188 control chromosomes in the GnomAD database, including 509 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 0.051 ( 509 hom., cov: 32)

Consequence

ENSG00000254092
ENST00000657734.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.122

Publications

0 publications found

Variant links:

Genes affected

ENSG00000254092 (HGNC:):

ENSG00000254092 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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 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
ENSG00000254092	ENST00000657734.1 link	n.1326+32485C>G		intron_variant	Intron 2 of 4
ENSG00000254092	ENST00000659453.1 link	n.1639+32485C>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.0507

AC:

7705

AN:

152070

Hom.:

508

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0269

Gnomad ASJ

AF:

0.0468

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00914

Gnomad FIN

AF:

0.000565

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.00690

Gnomad OTH

AF:

0.0513

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

GnomAD4 genome

AF:

0.0507

AC:

7721

AN:

152188

Hom.:

509

Cov.:

AF XY:

0.0480

AC XY:

3575

AN XY:

74410

show subpopulations

African (AFR)

AF:

0.157

AC:

6502

AN:

41502

American (AMR)

AF:

0.0269

AC:

411

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0468

AC:

162

AN:

3464

East Asian (EAS)

AF:

0.00

AC:

AN:

5168

South Asian (SAS)

AF:

0.00936

AC:

AN:

4808

European-Finnish (FIN)

AF:

0.000565

AC:

AN:

10618

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00690

AC:

469

AN:

68012

Other (OTH)

AF:

0.0508

AC:

107

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

341

682

1024

1365

1706

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

152

228

304

380

<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:

0.0316

Hom.:

Bravo

AF:

0.0579

Asia WGS

AF:

0.0110

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.4

(source)

DANN

Benign

0.47

PhyloP100

0.12

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