Genetic Variant ENSG00000299795:n.60-327G>T (chr17-2530730-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000766425.1(ENSG00000299795):n.60-327G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 151,720 control chromosomes in the GnomAD database, including 2,111 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 0.16 ( 2111 hom., cov: 31)

Consequence

ENSG00000299795
ENST00000766425.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.414

Publications

4 publications found

Variant links:

Genes affected

ENSG00000299795 (HGNC:):

ENSG00000299795 links:

Genome browser will be placed here

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=-0.99).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.224 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
ENSG00000299795	ENST00000766425.1 link	n.60-327G>T		intron_variant	Intron 1 of 3
ENSG00000299795	ENST00000766426.1 link	n.69+18697G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.165

AC:

24947

AN:

151602

Hom.:

2108

Cov.:

show subpopulations

Gnomad AFR

AF:

0.192

Gnomad AMI

AF:

0.0471

Gnomad AMR

AF:

0.184

Gnomad ASJ

AF:

0.104

Gnomad EAS

AF:

0.197

Gnomad SAS

AF:

0.236

Gnomad FIN

AF:

0.165

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.141

Gnomad OTH

AF:

0.156

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

GnomAD4 genome

AF:

0.164

AC:

24953

AN:

151720

Hom.:

2111

Cov.:

AF XY:

0.166

AC XY:

12335

AN XY:

74156

show subpopulations

African (AFR)

AF:

0.192

AC:

7913

AN:

41270

American (AMR)

AF:

0.184

AC:

2794

AN:

15206

Ashkenazi Jewish (ASJ)

AF:

0.104

AC:

360

AN:

3468

East Asian (EAS)

AF:

0.196

AC:

1012

AN:

5158

South Asian (SAS)

AF:

0.236

AC:

1136

AN:

4818

European-Finnish (FIN)

AF:

0.165

AC:

1732

AN:

10524

Middle Eastern (MID)

AF:

0.133

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.141

AC:

9597

AN:

67962

Other (OTH)

AF:

0.155

AC:

327

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1055

2111

3166

4222

5277

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

280

560

840

1120

1400

<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:

0.149

Hom.:

5511

Bravo

AF:

0.166

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.48

(source)

DANN

Benign

0.31

PhyloP100

-0.41

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