Genetic Variant ENSG00000275016:n.27-34401G>T (chr15-95681992-G-T) – 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.27-34401G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 151,924 control chromosomes in the GnomAD database, including 10,316 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 0.34 ( 10316 hom., cov: 32)

Consequence

ENSG00000275016
ENST00000611285.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.67

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=-0.45).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.452 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.27-34401G>T	intron_variant	Intron 1 of 1	5
ENSG00000275016	ENST00000612595.2 link	n.204+43473G>T	intron_variant	Intron 1 of 2	5
ENSG00000275016	ENST00000614344.6 link	n.201+43473G>T	intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes

AF:

0.341

AC:

51800

AN:

151804

Hom.:

10321

Cov.:

show subpopulations

Gnomad AFR

AF:

0.141

Gnomad AMI

AF:

0.546

Gnomad AMR

AF:

0.338

Gnomad ASJ

AF:

0.426

Gnomad EAS

AF:

0.235

Gnomad SAS

AF:

0.251

Gnomad FIN

AF:

0.426

Gnomad MID

AF:

0.484

Gnomad NFE

AF:

0.456

Gnomad OTH

AF:

0.386

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

GnomAD4 genome

AF:

0.341

AC:

51808

AN:

151924

Hom.:

10316

Cov.:

AF XY:

0.337

AC XY:

25015

AN XY:

74242

show subpopulations

African (AFR)

AF:

0.141

AC:

5843

AN:

41422

American (AMR)

AF:

0.338

AC:

5158

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.426

AC:

1478

AN:

3470

East Asian (EAS)

AF:

0.235

AC:

1209

AN:

5154

South Asian (SAS)

AF:

0.251

AC:

1210

AN:

4820

European-Finnish (FIN)

AF:

0.426

AC:

4475

AN:

10516

Middle Eastern (MID)

AF:

0.490

AC:

143

AN:

292

European-Non Finnish (NFE)

AF:

0.456

AC:

30987

AN:

67958

Other (OTH)

AF:

0.382

AC:

807

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1623

3247

4870

6494

8117

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

502

1004

1506

2008

2510

<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:

0.415

Hom.:

58558

Bravo

AF:

0.325

Asia WGS

AF:

0.237

AC:

825

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

8.7

(source)

DANN

Benign

0.56

PhyloP100

1.7

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