Genetic Variant ENSG00000285666:n.1020-10431A>G (chr7-76829719-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000648393.1(ENSG00000285666):n.1020-10431A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0339 in 147,788 control chromosomes in the GnomAD database, including 117 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 0.034 ( 117 hom., cov: 35)

Consequence

ENSG00000285666
ENST00000648393.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.258

Publications

2 publications found

Variant links:

Genes affected

ENSG00000285666 (HGNC:):

ENSG00000285666 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0926 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000285666	ENST00000648393.1 link	n.1020-10431A>G	intron_variant	Intron 6 of 7
ENSG00000285666	ENST00000827560.1 link	n.483-3368A>G	intron_variant	Intron 3 of 4
ENSG00000285666	ENST00000827561.1 link	n.490-3368A>G	intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes

AF:

0.0338

AC:

4997

AN:

147692

Hom.:

115

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0947

Gnomad AMI

AF:

0.00227

Gnomad AMR

AF:

0.0171

Gnomad ASJ

AF:

0.0187

Gnomad EAS

AF:

0.0142

Gnomad SAS

AF:

0.00943

Gnomad FIN

AF:

0.0134

Gnomad MID

AF:

0.0304

Gnomad NFE

AF:

0.00854

Gnomad OTH

AF:

0.0277

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

GnomAD4 genome

AF:

0.0339

AC:

5017

AN:

147788

Hom.:

117

Cov.:

AF XY:

0.0327

AC XY:

2365

AN XY:

72270

show subpopulations

African (AFR)

AF:

0.0951

AC:

3819

AN:

40144

American (AMR)

AF:

0.0171

AC:

256

AN:

14992

Ashkenazi Jewish (ASJ)

AF:

0.0187

AC:

AN:

3362

East Asian (EAS)

AF:

0.0137

AC:

AN:

5188

South Asian (SAS)

AF:

0.00901

AC:

AN:

4660

European-Finnish (FIN)

AF:

0.0134

AC:

135

AN:

10070

Middle Eastern (MID)

AF:

0.0292

AC:

AN:

274

European-Non Finnish (NFE)

AF:

0.00854

AC:

565

AN:

66174

Other (OTH)

AF:

0.0274

AC:

AN:

2044

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.443

Heterozygous variant carriers

154

308

461

615

769

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

162

216

270

<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:

0.0304

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

4.7

(source)

DANN

Benign

0.24

PhyloP100

0.26

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