rs10868525

Variant names:

• chr9-87003113-T-C
• rs10868525
• ENST00000846239.1:n.308-8461T>C

Variant summary

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

The ENST00000846239.1(GAS1RR):​n.308-8461T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 151,910 control chromosomes in the GnomAD database, including 26,176 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 0.58 (26176 hom., cov: 31)
• Consequence: GAS1RR ENST00000846239.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000846239.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAS1RR	ENST00000846239.1		n.308-8461T>C		intron	N/A
	GAS1RR	ENST00000846240.1		n.561-8461T>C		intron	N/A
	GAS1RR	ENST00000846241.1		n.304-5504T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88651 AN: 151792 Hom.: 26168 Cov.: 31

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.584 AC: 88691 AN: 151910 Hom.: 26176 Cov.: 31 AF XY: 0.578 AC XY: 42916 AN XY: 74238

African (AFR) AF: 0.524 AC: 21697 AN: 41410

American (AMR) AF: 0.586 AC: 8941 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 2409 AN: 3470

East Asian (EAS) AF: 0.544 AC: 2799 AN: 5144

South Asian (SAS) AF: 0.545 AC: 2625 AN: 4818

European-Finnish (FIN) AF: 0.540 AC: 5698 AN: 10556

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42424 AN: 67932

Other (OTH) AF: 0.603 AC: 1271 AN: 2108

Alfa AF: 0.599 Hom.: 4974

Bravo AF: 0.587

Asia WGS AF: 0.501 AC: 1745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.0
DANN	Benign	0.86
PhyloP100		0.051

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: rs10868525;

hg19: chr9-89618028;