chr9-86948791-T-C

Position:

• chr9-86948791-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_049794.1(GAS1RR):​n.94T>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 NR_049794.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
GAS1RR	NR_049794.1	n.94T>C		non_coding_transcript_exon_variant	1/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAS1RR	ENST00000415801.1	n.93T>C		non_coding_transcript_exon_variant	1/7	1
GAS1RR	ENST00000654660.2	n.163T>C		non_coding_transcript_exon_variant	1/2
GAS1RR	ENST00000701854.1	n.108T>C		non_coding_transcript_exon_variant	1/2

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

Gnomad4 AMR exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.313

Gnomad4 OTH exome AF: 0.500

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

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.423

Alfa AF: 0.287 Hom.: 958

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
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2301361; hg19: chr9-89563706;