Genetic Variant GAS1RR:n.93T>C (chr9-86948791-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.93T>C 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 0.441 in 152,206 control chromosomes in the GnomAD database, including 16,170 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 0.44 ( 16169 hom., cov: 33)

Exomes 𝑓: 0.32 ( 1 hom. )

Consequence

GAS1RR
ENST00000415801.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.140

Publications

0 publications found

Variant links:

Genes affected

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

GAS1RR links:

ENSG00000310004 (HGNC:):

ENSG00000310004 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=-0.78).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GAS1RR	NR_049794.1 link	n.94T>C		non_coding_transcript_exon_variant	Exon 1 of 7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
GAS1RR	ENST00000415801.1 link	n.93T>C	non_coding_transcript_exon_variant	Exon 1 of 7	1
GAS1RR	ENST00000654660.3 link	n.181T>C	non_coding_transcript_exon_variant	Exon 1 of 2
GAS1RR	ENST00000701854.2 link	n.152T>C	non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.441

AC:

67099

AN:

152066

Hom.:

16138

Cov.:

show subpopulations

Gnomad AFR

AF:

0.639

Gnomad AMI

AF:

0.325

Gnomad AMR

AF:

0.324

Gnomad ASJ

AF:

0.373

Gnomad EAS

AF:

0.447

Gnomad SAS

AF:

0.369

Gnomad FIN

AF:

0.416

Gnomad MID

AF:

0.459

Gnomad NFE

AF:

0.361

Gnomad OTH

AF:

0.424

GnomAD4 exome

AF:

0.318

AC:

AN:

Hom.:

Cov.:

AF XY:

0.357

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.313

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.585

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.441

AC:

67170

AN:

152184

Hom.:

16169

Cov.:

AF XY:

0.443

AC XY:

32921

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.639

AC:

26551

AN:

41546

American (AMR)

AF:

0.324

AC:

4949

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.373

AC:

1294

AN:

3472

East Asian (EAS)

AF:

0.447

AC:

2302

AN:

5152

South Asian (SAS)

AF:

0.372

AC:

1796

AN:

4826

European-Finnish (FIN)

AF:

0.416

AC:

4412

AN:

10594

Middle Eastern (MID)

AF:

0.469

AC:

138

AN:

294

European-Non Finnish (NFE)

AF:

0.361

AC:

24540

AN:

67986

Other (OTH)

AF:

0.423

AC:

894

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1893

3785

5678

7570

9463

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

608

1216

1824

2432

3040

<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:

0.302

Hom.:

1117

Bravo

AF:

0.443

Asia WGS

AF:

0.407

AC:

1420

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

7.5

(source)

DANN

Benign

0.64

PhyloP100

0.14

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over