Genetic Variant ENST00000845015.1:n.253+12063C>T (chr2-17181301-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 ENST00000845015.1(ENSG00000309887):n.253+12063C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0905 in 152,244 control chromosomes in the GnomAD database, including 2,115 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 0.091 ( 2115 hom., cov: 32)

Consequence

ENSG00000309887
ENST00000845015.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.141

Publications

13 publications found

Variant links:

Genes affected

ENSG00000309887 (HGNC:):

ENSG00000309887 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 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
ENSG00000309887	ENST00000845015.1 link	n.253+12063C>T		intron_variant	Intron 1 of 2
ENSG00000309902	ENST00000845391.1 link	n.216+2104G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0905

AC:

13768

AN:

152126

Hom.:

2110

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0168

Gnomad AMI

AF:

0.119

Gnomad AMR

AF:

0.159

Gnomad ASJ

AF:

0.0323

Gnomad EAS

AF:

0.753

Gnomad SAS

AF:

0.209

Gnomad FIN

AF:

0.135

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0564

Gnomad OTH

AF:

0.112

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

GnomAD4 genome

AF:

0.0905

AC:

13785

AN:

152244

Hom.:

2115

Cov.:

AF XY:

0.100

AC XY:

7472

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.0167

AC:

695

AN:

41564

American (AMR)

AF:

0.159

AC:

2437

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0323

AC:

112

AN:

3468

East Asian (EAS)

AF:

0.753

AC:

3896

AN:

5172

South Asian (SAS)

AF:

0.209

AC:

1005

AN:

4820

European-Finnish (FIN)

AF:

0.135

AC:

1432

AN:

10606

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0565

AC:

3840

AN:

68012

Other (OTH)

AF:

0.119

AC:

252

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

511

1023

1534

2046

2557

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

154

308

462

616

770

<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:

0.0774

Hom.:

2522

Bravo

AF:

0.0934

Asia WGS

AF:

0.456

AC:

1581

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.9

(source)

DANN

Benign

0.30

PhyloP100

0.14

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