Genetic Variant ENSG00000257526:n.703+3996A>G (chr12-76695101-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000832799.1(ENSG00000257526):n.703+3996A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 151,998 control chromosomes in the GnomAD database, including 29,555 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 0.62 ( 29555 hom., cov: 31)

Consequence

ENSG00000257526
ENST00000832799.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.803

Variant links:

Genes affected

ENSG00000257526 (HGNC:):

ENSG00000257526 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=-1.02).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.68 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
ENSG00000257526	ENST00000832799.1 link	n.703+3996A>G		intron_variant	Intron 5 of 5
ENSG00000257526	ENST00000832800.1 link	n.565-22806A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.621

AC:

94243

AN:

151880

Hom.:

29541

Cov.:

show subpopulations

Gnomad AFR

AF:

0.687

Gnomad AMI

AF:

0.541

Gnomad AMR

AF:

0.553

Gnomad ASJ

AF:

0.626

Gnomad EAS

AF:

0.623

Gnomad SAS

AF:

0.567

Gnomad FIN

AF:

0.601

Gnomad MID

AF:

0.617

Gnomad NFE

AF:

0.603

Gnomad OTH

AF:

0.616

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

GnomAD4 genome

AF:

0.620

AC:

94289

AN:

151998

Hom.:

29555

Cov.:

AF XY:

0.618

AC XY:

45875

AN XY:

74254

show subpopulations

African (AFR)

AF:

0.687

AC:

28471

AN:

41456

American (AMR)

AF:

0.553

AC:

8453

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.626

AC:

2173

AN:

3472

East Asian (EAS)

AF:

0.623

AC:

3206

AN:

5150

South Asian (SAS)

AF:

0.567

AC:

2730

AN:

4816

European-Finnish (FIN)

AF:

0.601

AC:

6336

AN:

10542

Middle Eastern (MID)

AF:

0.609

AC:

179

AN:

294

European-Non Finnish (NFE)

AF:

0.603

AC:

40960

AN:

67958

Other (OTH)

AF:

0.611

AC:

1291

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1834

3668

5501

7335

9169

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.606

Hom.:

118056

Bravo

AF:

0.620

Asia WGS

AF:

0.566

AC:

1971

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.6

(source)

DANN

Benign

0.28

PhyloP100

-0.80

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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chr12-76695101-A-G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over