Genetic Variant ENSG00000297132:n.379-1261G>A (chr6-75531811-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000745740.1(ENSG00000297132):n.379-1261G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,080 control chromosomes in the GnomAD database, including 1,036 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 0.12 ( 1036 hom., cov: 33)

Consequence

ENSG00000297132
ENST00000745740.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.398

Publications

29 publications found

Variant links:

Genes affected

ENSG00000297132 (HGNC:):

ENSG00000297132 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000297132	ENST00000745740.1 link	n.379-1261G>A	intron_variant	Intron 2 of 3
ENSG00000297132	ENST00000745741.1 link	n.387-1261G>A	intron_variant	Intron 2 of 3
ENSG00000297132	ENST00000745742.1 link	n.373-1261G>A	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.116

AC:

17615

AN:

151962

Hom.:

1034

Cov.:

show subpopulations

Gnomad AFR

AF:

0.126

Gnomad AMI

AF:

0.0976

Gnomad AMR

AF:

0.0974

Gnomad ASJ

AF:

0.0942

Gnomad EAS

AF:

0.103

Gnomad SAS

AF:

0.107

Gnomad FIN

AF:

0.129

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.115

Gnomad OTH

AF:

0.115

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

GnomAD4 genome

AF:

0.116

AC:

17629

AN:

152080

Hom.:

1036

Cov.:

AF XY:

0.116

AC XY:

8598

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.126

AC:

5226

AN:

41494

American (AMR)

AF:

0.0973

AC:

1486

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0942

AC:

327

AN:

3470

East Asian (EAS)

AF:

0.103

AC:

531

AN:

5176

South Asian (SAS)

AF:

0.107

AC:

516

AN:

4822

European-Finnish (FIN)

AF:

0.129

AC:

1365

AN:

10542

Middle Eastern (MID)

AF:

0.0986

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.115

AC:

7820

AN:

67984

Other (OTH)

AF:

0.114

AC:

240

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

812

1623

2435

3246

4058

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

190

380

570

760

950

<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:

0.110

Hom.:

522

Bravo

AF:

0.112

Asia WGS

AF:

0.0890

AC:

312

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.5

(source)

DANN

Benign

0.75

PhyloP100

-0.40

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