Genetic Variant ENST00000741265.1:n.292+2698G>A (chr13-90718206-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000741265.1(ENSG00000296712):n.292+2698G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.964 in 152,142 control chromosomes in the GnomAD database, including 70,913 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 0.96 ( 70913 hom., cov: 33)

Consequence

ENSG00000296712
ENST00000741265.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.723

Publications

2 publications found

Variant links:

Genes affected

ENSG00000296712 (HGNC:):

ENSG00000296712 links:

Genome browser will be placed here

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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000296712	ENST00000741265.1 link	n.292+2698G>A	intron_variant	Intron 3 of 4
ENSG00000296744	ENST00000741517.1 link	n.356-338C>T	intron_variant	Intron 2 of 2
ENSG00000296744	ENST00000741518.1 link	n.542-338C>T	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.964

AC:

146535

AN:

152024

Hom.:

70857

Cov.:

show subpopulations

Gnomad AFR

AF:

0.874

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.987

Gnomad ASJ

AF:

1.00

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

1.00

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

0.994

Gnomad NFE

AF:

1.00

Gnomad OTH

AF:

0.968

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

GnomAD4 genome

AF:

0.964

AC:

146648

AN:

152142

Hom.:

70913

Cov.:

AF XY:

0.966

AC XY:

71819

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.875

AC:

36306

AN:

41508

American (AMR)

AF:

0.987

AC:

15047

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

3468

AN:

3468

East Asian (EAS)

AF:

1.00

AC:

5176

AN:

5176

South Asian (SAS)

AF:

1.00

AC:

4828

AN:

4828

European-Finnish (FIN)

AF:

1.00

AC:

10628

AN:

10628

Middle Eastern (MID)

AF:

0.993

AC:

292

AN:

294

European-Non Finnish (NFE)

AF:

1.00

AC:

67948

AN:

67966

Other (OTH)

AF:

0.968

AC:

2043

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

243

486

728

971

1214

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

912

1824

2736

3648

4560

<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:

0.975

Hom.:

10331

Bravo

AF:

0.959

Asia WGS

AF:

0.996

AC:

3465

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.88

(source)

DANN

Benign

0.18

PhyloP100

-0.72

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