dbSNP rs10494676: ENSG00000285280:n.201+9867G>T (chr1-192915745-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000644058.2(ENSG00000285280):n.201+9867G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0951 in 151,932 control chromosomes in the GnomAD database, including 1,766 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 0.095 ( 1766 hom., cov: 33)

Consequence

ENSG00000285280
ENST00000644058.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.925

Publications

2 publications found

Variant links:

Genes affected

ENSG00000285280 (HGNC:49018): (RSG2 antisense RNA 1)

ENSG00000285280 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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000285280	ENST00000644058.2 link	n.201+9867G>T	intron_variant	Intron 1 of 5
ENSG00000285280	ENST00000644134.1 link	n.104+9867G>T	intron_variant	Intron 1 of 6
ENSG00000285280	ENST00000644436.1 link	n.105-4264G>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0950

AC:

14417

AN:

151814

Hom.:

1761

Cov.:

show subpopulations

Gnomad AFR

AF:

0.288

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0514

Gnomad ASJ

AF:

0.0542

Gnomad EAS

AF:

0.00193

Gnomad SAS

AF:

0.0303

Gnomad FIN

AF:

0.00797

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.0165

Gnomad OTH

AF:

0.0747

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

GnomAD4 genome

AF:

0.0951

AC:

14442

AN:

151932

Hom.:

1766

Cov.:

AF XY:

0.0929

AC XY:

6896

AN XY:

74266

show subpopulations

African (AFR)

AF:

0.288

AC:

11932

AN:

41404

American (AMR)

AF:

0.0513

AC:

783

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.0542

AC:

188

AN:

3468

East Asian (EAS)

AF:

0.00193

AC:

AN:

5174

South Asian (SAS)

AF:

0.0305

AC:

147

AN:

4816

European-Finnish (FIN)

AF:

0.00797

AC:

AN:

10540

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0165

AC:

1123

AN:

67946

Other (OTH)

AF:

0.0739

AC:

156

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

558

1117

1675

2234

2792

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

138

276

414

552

690

<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:

0.00377

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.7

(source)

DANN

Benign

0.44

PhyloP100

0.93

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