Genetic Variant GAS1RR:n.308-8461T>C (chr9-87003113-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 ENST00000846239.1(GAS1RR):n.308-8461T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 151,910 control chromosomes in the GnomAD database, including 26,176 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 0.58 ( 26176 hom., cov: 31)

Consequence

GAS1RR
ENST00000846239.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0510

Publications

2 publications found

Variant links:

Genes affected

GAS1RR (HGNC:52261): (GAS1 adjacent regulatory RNA)

GAS1RR 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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
GAS1RR	ENST00000846239.1 link	n.308-8461T>C	intron_variant	Intron 1 of 1
GAS1RR	ENST00000846240.1 link	n.561-8461T>C	intron_variant	Intron 2 of 2
GAS1RR	ENST00000846241.1 link	n.304-5504T>C	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.584

AC:

88651

AN:

151792

Hom.:

26168

Cov.:

show subpopulations

Gnomad AFR

AF:

0.524

Gnomad AMI

AF:

0.701

Gnomad AMR

AF:

0.586

Gnomad ASJ

AF:

0.694

Gnomad EAS

AF:

0.543

Gnomad SAS

AF:

0.544

Gnomad FIN

AF:

0.540

Gnomad MID

AF:

0.652

Gnomad NFE

AF:

0.625

Gnomad OTH

AF:

0.605

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

GnomAD4 genome

AF:

0.584

AC:

88691

AN:

151910

Hom.:

26176

Cov.:

AF XY:

0.578

AC XY:

42916

AN XY:

74238

show subpopulations

African (AFR)

AF:

0.524

AC:

21697

AN:

41410

American (AMR)

AF:

0.586

AC:

8941

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.694

AC:

2409

AN:

3470

East Asian (EAS)

AF:

0.544

AC:

2799

AN:

5144

South Asian (SAS)

AF:

0.545

AC:

2625

AN:

4818

European-Finnish (FIN)

AF:

0.540

AC:

5698

AN:

10556

Middle Eastern (MID)

AF:

0.643

AC:

189

AN:

294

European-Non Finnish (NFE)

AF:

0.625

AC:

42424

AN:

67932

Other (OTH)

AF:

0.603

AC:

1271

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1849

3698

5548

7397

9246

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.599

Hom.:

4974

Bravo

AF:

0.587

Asia WGS

AF:

0.501

AC:

1745

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

6.0

(source)

DANN

Benign

0.86

PhyloP100

0.051

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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chr9-87003113-T-C

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