Genetic Variant ENST00000615635.1:n.116-5797G>T (chr13-109801260-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

-12

BP4_StrongBA1

The ENST00000615635.1(ENSG00000275741):n.116-5797G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 152,128 control chromosomes in the GnomAD database, including 52,254 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 0.83 ( 52254 hom., cov: 33)

Consequence

ENSG00000275741
ENST00000615635.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.524

Publications

11 publications found

Variant links:

Genes affected

ENSG00000275741 (HGNC:):

ENSG00000275741 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=-1.0).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370360	XR_931723.3 link	n.200+4091G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000275741	ENST00000615635.1 link	n.116-5797G>T		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes

AF:

0.828

AC:

125847

AN:

152010

Hom.:

52206

Cov.:

show subpopulations

Gnomad AFR

AF:

0.820

Gnomad AMI

AF:

0.823

Gnomad AMR

AF:

0.860

Gnomad ASJ

AF:

0.859

Gnomad EAS

AF:

0.678

Gnomad SAS

AF:

0.776

Gnomad FIN

AF:

0.849

Gnomad MID

AF:

0.880

Gnomad NFE

AF:

0.836

Gnomad OTH

AF:

0.823

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

GnomAD4 genome

AF:

0.828

AC:

125952

AN:

152128

Hom.:

52254

Cov.:

AF XY:

0.828

AC XY:

61566

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.820

AC:

34006

AN:

41460

American (AMR)

AF:

0.860

AC:

13159

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.859

AC:

2984

AN:

3472

East Asian (EAS)

AF:

0.677

AC:

3500

AN:

5168

South Asian (SAS)

AF:

0.776

AC:

3744

AN:

4824

European-Finnish (FIN)

AF:

0.849

AC:

8988

AN:

10586

Middle Eastern (MID)

AF:

0.874

AC:

257

AN:

294

European-Non Finnish (NFE)

AF:

0.836

AC:

56827

AN:

67996

Other (OTH)

AF:

0.821

AC:

1736

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1134

2268

3403

4537

5671

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

886

1772

2658

3544

4430

<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:

0.833

Hom.:

28571

Bravo

AF:

0.829

Asia WGS

AF:

0.730

AC:

2504

AN:

3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.21

(source)

DANN

Benign

0.41

PhyloP100

-0.52

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