rs2487032

chr9-104941653-G-Achr9-104941653-G-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.773

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.559

Alfa AF: 0.533 Hom.: 4574

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2487032; hg19: chr9-107703934;