Genetic Variant ENST00000755956.1:n.429-17515G>A (chr1-87482840-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 ENST00000755956.1(ENSG00000298492):n.429-17515G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0635 in 151,896 control chromosomes in the GnomAD database, including 353 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 0.063 ( 353 hom., cov: 33)

Consequence

ENSG00000298492
ENST00000755956.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0290

Publications

2 publications found

Variant links:

Genes affected

ENSG00000298492 (HGNC:):

ENSG00000298492 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 = 0.0807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000298492	ENST00000755956.1 link	n.429-17515G>A	intron_variant	Intron 2 of 7
ENSG00000298492	ENST00000755957.1 link	n.244+31739G>A	intron_variant	Intron 1 of 3
ENSG00000298492	ENST00000755958.1 link	n.404+31739G>A	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.0635

AC:

9639

AN:

151778

Hom.:

353

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0392

Gnomad AMI

AF:

0.0890

Gnomad AMR

AF:

0.0602

Gnomad ASJ

AF:

0.0815

Gnomad EAS

AF:

0.00579

Gnomad SAS

AF:

0.0403

Gnomad FIN

AF:

0.0715

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0825

Gnomad OTH

AF:

0.0679

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

GnomAD4 genome

AF:

0.0635

AC:

9641

AN:

151896

Hom.:

353

Cov.:

AF XY:

0.0612

AC XY:

4540

AN XY:

74206

show subpopulations

African (AFR)

AF:

0.0391

AC:

1623

AN:

41476

American (AMR)

AF:

0.0601

AC:

917

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.0815

AC:

282

AN:

3462

East Asian (EAS)

AF:

0.00581

AC:

AN:

5166

South Asian (SAS)

AF:

0.0401

AC:

193

AN:

4814

European-Finnish (FIN)

AF:

0.0715

AC:

752

AN:

10516

Middle Eastern (MID)

AF:

0.0612

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0825

AC:

5601

AN:

67884

Other (OTH)

AF:

0.0682

AC:

144

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

460

920

1381

1841

2301

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

110

220

330

440

550

<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:

0.0638

Hom.:

Bravo

AF:

0.0619

Asia WGS

AF:

0.0350

AC:

122

AN:

3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.87

(source)

DANN

Benign

0.43

PhyloP100

-0.029

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