chr9-86948791-T-C

Variant names:

• chr9-86948791-T-C
• rs2301361
• ENST00000415801.1:n.93T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140
• Publications: 0 publications found

Genes affected

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

ENSG00000310004 (HGNC:):

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000415801.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAS1RR	NR_049794.1		n.94T>C		non_coding_transcript_exon	Exon 1 of 7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAS1RR	ENST00000415801.1	TSL:1	n.93T>C		non_coding_transcript_exon	Exon 1 of 7
	GAS1RR	ENST00000654660.3		n.181T>C		non_coding_transcript_exon	Exon 1 of 2
	GAS1RR	ENST00000701854.2		n.152T>C		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.441 AC: 67099 AN: 152066 Hom.: 16138 Cov.: 33

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: 7 AN: 22 Hom.: 1 Cov.: 0 AF XY: 0.357 AC XY: 5 AN XY: 14

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.313 AC: 5 AN: 16

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.441 AC: 67170 AN: 152184 Hom.: 16169 Cov.: 33 AF XY: 0.443 AC XY: 32921 AN XY: 74394

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

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.5
DANN	Benign	0.64
PhyloP100		0.14

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2301361;

hg19: chr9-89563706;