Genetic Variant GAS1RR:n.857+1477T>C (chr9-86990383-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 ENST00000415801.1(GAS1RR):n.857+1477T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 152,248 control chromosomes in the GnomAD database, including 52,385 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 0.83 ( 52385 hom., cov: 34)

Consequence

GAS1RR
ENST00000415801.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00600

Publications

5 publications found

Variant links:

Genes affected

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

GAS1RR 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GAS1RR	NR_049794.1 link	n.858+1477T>C		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
GAS1RR	ENST00000415801.1 link	n.857+1477T>C	intron_variant	Intron 5 of 6	1
GAS1RR	ENST00000846239.1 link	n.308-21191T>C	intron_variant	Intron 1 of 1
GAS1RR	ENST00000846240.1 link	n.561-21191T>C	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.827

AC:

125831

AN:

152130

Hom.:

52332

Cov.:

show subpopulations

Gnomad AFR

AF:

0.903

Gnomad AMI

AF:

0.624

Gnomad AMR

AF:

0.822

Gnomad ASJ

AF:

0.833

Gnomad EAS

AF:

0.997

Gnomad SAS

AF:

0.844

Gnomad FIN

AF:

0.773

Gnomad MID

AF:

0.741

Gnomad NFE

AF:

0.780

Gnomad OTH

AF:

0.808

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

GnomAD4 genome

AF:

0.827

AC:

125939

AN:

152248

Hom.:

52385

Cov.:

AF XY:

0.828

AC XY:

61643

AN XY:

74442

show subpopulations

African (AFR)

AF:

0.903

AC:

37509

AN:

41556

American (AMR)

AF:

0.822

AC:

12583

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.833

AC:

2892

AN:

3472

East Asian (EAS)

AF:

0.997

AC:

5170

AN:

5184

South Asian (SAS)

AF:

0.843

AC:

4067

AN:

4826

European-Finnish (FIN)

AF:

0.773

AC:

8185

AN:

10588

Middle Eastern (MID)

AF:

0.731

AC:

215

AN:

294

European-Non Finnish (NFE)

AF:

0.780

AC:

53037

AN:

68006

Other (OTH)

AF:

0.811

AC:

1713

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1113

2225

3338

4450

5563

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

888

1776

2664

3552

4440

<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:

0.809

Hom.:

12652

Bravo

AF:

0.834

Asia WGS

AF:

0.925

AC:

3219

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.3

(source)

DANN

Benign

0.76

PhyloP100

-0.0060

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