rs2487032

Variant names:

• chr9-104941653-G-A
• rs2487032

Your query was ambiguous. Multiple possible variants found:

• chr9-104941653-G-A
• chr9-104941653-G-C
• chr9-104941653-G-T

Variant summary

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

The variant allele was found at a frequency of 0.58 in 151,870 control chromosomes in the GnomAD database, including 26,713 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 (26713 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490
• Publications: 32 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88027 AN: 151752 Hom.: 26694 Cov.: 32

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.580 AC: 88093 AN: 151870 Hom.: 26713 Cov.: 32 AF XY: 0.579 AC XY: 42990 AN XY: 74200

African (AFR) AF: 0.773 AC: 31981 AN: 41390

American (AMR) AF: 0.489 AC: 7469 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2152 AN: 3468

East Asian (EAS) AF: 0.479 AC: 2474 AN: 5162

South Asian (SAS) AF: 0.570 AC: 2750 AN: 4822

European-Finnish (FIN) AF: 0.516 AC: 5444 AN: 10560

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 34016 AN: 67894

Other (OTH) AF: 0.559 AC: 1180 AN: 2112

Alfa AF: 0.517 Hom.: 29419

Bravo AF: 0.584

Asia WGS AF: 0.532 AC: 1849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.6
DANN	Benign	0.60
PhyloP100		0.049

Splicing

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

Other links and lift over

dbSNP: rs2487032; hg19: chr9-107703934;