Genetic Variant ENST00000611285.1:n.26+8734G>A (chr15-95647253-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000611285.1(ENSG00000275016):n.26+8734G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,224 control chromosomes in the GnomAD database, including 2,575 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 0.14 ( 2575 hom., cov: 34)

Consequence

ENSG00000275016
ENST00000611285.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.38

Publications

3 publications found

Variant links:

Genes affected

ENSG00000275016 (HGNC:):

ENSG00000275016 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.25).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000275016	ENST00000611285.1 link	n.26+8734G>A	intron_variant	Intron 1 of 1	5
ENSG00000275016	ENST00000612595.2 link	n.204+8734G>A	intron_variant	Intron 1 of 2	5
ENSG00000275016	ENST00000614344.6 link	n.201+8734G>A	intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes

AF:

0.139

AC:

21155

AN:

152106

Hom.:

2571

Cov.:

show subpopulations

Gnomad AFR

AF:

0.322

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.0811

Gnomad ASJ

AF:

0.0164

Gnomad EAS

AF:

0.229

Gnomad SAS

AF:

0.139

Gnomad FIN

AF:

0.0859

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0514

Gnomad OTH

AF:

0.110

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

GnomAD4 genome

AF:

0.139

AC:

21181

AN:

152224

Hom.:

2575

Cov.:

AF XY:

0.141

AC XY:

10517

AN XY:

74430

show subpopulations

African (AFR)

AF:

0.322

AC:

13370

AN:

41522

American (AMR)

AF:

0.0808

AC:

1235

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0164

AC:

AN:

3470

East Asian (EAS)

AF:

0.229

AC:

1182

AN:

5172

South Asian (SAS)

AF:

0.138

AC:

665

AN:

4818

European-Finnish (FIN)

AF:

0.0859

AC:

912

AN:

10612

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0515

AC:

3500

AN:

68020

Other (OTH)

AF:

0.110

AC:

232

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

850

1699

2549

3398

4248

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

216

432

648

864

1080

<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:

0.0713

Hom.:

461

Bravo

AF:

0.146

Asia WGS

AF:

0.203

AC:

704

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.25

CADD

Benign

(source)

DANN

Benign

0.76

PhyloP100

3.4

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