Genetic Variant ENST00000646875.2:n.37G>A (chr1-65703996-G-A) – 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.37G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 152,242 control chromosomes in the GnomAD database, including 25,629 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 0.57 ( 25603 hom., cov: 32)

Exomes 𝑓: 0.57 ( 26 hom. )

Consequence

ENSG00000285079
ENST00000646875.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.04

Publications

31 publications found

Variant links:

Genes affected

ENSG00000285079 (HGNC:):

ENSG00000285079 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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.618 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.37G>A	non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000285079	ENST00000760543.1 link	n.54G>A	non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000285079	ENST00000760544.1 link	n.-21G>A	upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.571

AC:

86779

AN:

151958

Hom.:

25598

Cov.:

show subpopulations

Gnomad AFR

AF:

0.565

Gnomad AMI

AF:

0.684

Gnomad AMR

AF:

0.536

Gnomad ASJ

AF:

0.625

Gnomad EAS

AF:

0.124

Gnomad SAS

AF:

0.537

Gnomad FIN

AF:

0.512

Gnomad MID

AF:

0.665

Gnomad NFE

AF:

0.623

Gnomad OTH

AF:

0.588

GnomAD4 exome

AF:

0.572

AC:

AN:

166

Hom.:

Cov.:

AF XY:

0.592

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.250

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.545

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.603

AC:

AN:

116

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.571

AC:

86815

AN:

152076

Hom.:

25603

Cov.:

AF XY:

0.562

AC XY:

41753

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.565

AC:

23413

AN:

41474

American (AMR)

AF:

0.536

AC:

8191

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.625

AC:

2169

AN:

3470

East Asian (EAS)

AF:

0.125

AC:

644

AN:

5170

South Asian (SAS)

AF:

0.539

AC:

2593

AN:

4810

European-Finnish (FIN)

AF:

0.512

AC:

5417

AN:

10570

Middle Eastern (MID)

AF:

0.650

AC:

191

AN:

294

European-Non Finnish (NFE)

AF:

0.623

AC:

42347

AN:

67972

Other (OTH)

AF:

0.581

AC:

1226

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1863

3726

5589

7452

9315

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

736

1472

2208

2944

3680

<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:

0.601

Hom.:

106153

Bravo

AF:

0.573

Asia WGS

AF:

0.367

AC:

1281

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

0.14

(source)

DANN

Benign

0.71

PhyloP100

-1.0

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