chr9-86958168-G-A

Position:

• chr9-86958168-G-A

Variant summary

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

The NR_049794.1(GAS1RR):​n.429+7169G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 152,030 control chromosomes in the GnomAD database, including 23,929 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 0.53 (23929 hom., cov: 33)
• Consequence: GAS1RR NR_049794.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAS1RR	NR_049794.1	n.429+7169G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAS1RR	ENST00000415801.1	n.428+7169G>A		intron_variant, non_coding_transcript_variant		1
GAS1RR	ENST00000701854.1	n.310+9175G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80218 AN: 151912 Hom.: 23872 Cov.: 33

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.528 AC: 80338 AN: 152030 Hom.: 23929 Cov.: 33 AF XY: 0.529 AC XY: 39341 AN XY: 74308

Gnomad4 AFR AF: 0.828

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.501

Alfa AF: 0.414 Hom.: 18559

Bravo AF: 0.548

Asia WGS AF: 0.468 AC: 1630 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.013
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: rs9792548; hg19: chr9-89573083;