Genetic Variant ENSG00000290870:n.2155+1517T>C (chr6-29855829-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 ENST00000647952.1(ENSG00000290870):n.2155+1517T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 152,098 control chromosomes in the GnomAD database, including 43,934 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 0.76 ( 43934 hom., cov: 32)

Consequence

ENSG00000290870
ENST00000647952.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.27

Publications

20 publications found

Variant links:

Genes affected

ENSG00000290870 (HGNC:):

ENSG00000290870 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 (EAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105375010	XR_926680.3 link	n.41+1517T>C	intron_variant	Intron 1 of 2
LOC105375010	XR_926681.2 link	n.41+1517T>C	intron_variant	Intron 1 of 3
LOC105375010	XR_926682.3 link	n.41+1517T>C	intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290870	ENST00000647952.1 link	n.2155+1517T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.759

AC:

115320

AN:

151978

Hom.:

43908

Cov.:

show subpopulations

Gnomad AFR

AF:

0.777

Gnomad AMI

AF:

0.829

Gnomad AMR

AF:

0.766

Gnomad ASJ

AF:

0.672

Gnomad EAS

AF:

0.826

Gnomad SAS

AF:

0.737

Gnomad FIN

AF:

0.652

Gnomad MID

AF:

0.763

Gnomad NFE

AF:

0.762

Gnomad OTH

AF:

0.765

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

GnomAD4 genome

AF:

0.759

AC:

115398

AN:

152098

Hom.:

43934

Cov.:

AF XY:

0.753

AC XY:

56023

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.777

AC:

32245

AN:

41484

American (AMR)

AF:

0.766

AC:

11697

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.672

AC:

2331

AN:

3470

East Asian (EAS)

AF:

0.826

AC:

4272

AN:

5172

South Asian (SAS)

AF:

0.735

AC:

3542

AN:

4822

European-Finnish (FIN)

AF:

0.652

AC:

6898

AN:

10576

Middle Eastern (MID)

AF:

0.752

AC:

221

AN:

294

European-Non Finnish (NFE)

AF:

0.762

AC:

51818

AN:

67980

Other (OTH)

AF:

0.768

AC:

1618

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1428

2857

4285

5714

7142

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

858

1716

2574

3432

4290

<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:

0.759

Hom.:

53175

Bravo

AF:

0.771

Asia WGS

AF:

0.796

AC:

2771

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

3.5

(source)

DANN

Benign

0.52

PhyloP100

-2.3

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