Genetic Variant ENSG00000285079:n.348-1564C>G (chr1-65709249-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000646875.2(ENSG00000285079):n.348-1564C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0112 in 152,282 control chromosomes in the GnomAD database, including 51 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 0.011 ( 51 hom., cov: 31)

Consequence

ENSG00000285079
ENST00000646875.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.739

Publications

0 publications found

Variant links:

Genes affected

ENSG00000285079 (HGNC:):

ENSG00000285079 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 (SAS) allele frequency at 95% confidence interval = 0.0886 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000285079	ENST00000646875.2 link	n.348-1564C>G	intron_variant	Intron 1 of 2
ENSG00000285079	ENST00000760543.1 link	n.364+4943C>G	intron_variant	Intron 1 of 1
ENSG00000285079	ENST00000760544.1 link	n.291-1564C>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0111

AC:

1691

AN:

152164

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00746

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00537

Gnomad ASJ

AF:

0.0222

Gnomad EAS

AF:

0.0669

Gnomad SAS

AF:

0.0964

Gnomad FIN

AF:

0.0212

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00225

Gnomad OTH

AF:

0.0139

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

GnomAD4 genome

AF:

0.0112

AC:

1707

AN:

152282

Hom.:

Cov.:

AF XY:

0.0135

AC XY:

1007

AN XY:

74474

show subpopulations

African (AFR)

AF:

0.00779

AC:

324

AN:

41570

American (AMR)

AF:

0.00536

AC:

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0222

AC:

AN:

3472

East Asian (EAS)

AF:

0.0668

AC:

346

AN:

5176

South Asian (SAS)

AF:

0.0959

AC:

462

AN:

4820

European-Finnish (FIN)

AF:

0.0212

AC:

225

AN:

10614

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00225

AC:

153

AN:

68018

Other (OTH)

AF:

0.0161

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

156

233

311

389

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

130

<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:

0.00603

Hom.:

Bravo

AF:

0.00772

Asia WGS

AF:

0.109

AC:

378

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

0.33

(source)

DANN

Benign

0.40

PhyloP100

-0.74

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