rs9287638

chr2-238785990-C-Achr2-238785990-C-T

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 0.402 in 151,382 control chromosomes in the GnomAD database, including 12,688 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 0.40 (12688 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 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: 0.402 AC: 60744 AN: 151264 Hom.: 12663 Cov.: 31

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.402 AC: 60826 AN: 151382 Hom.: 12688 Cov.: 31 AF XY: 0.408 AC XY: 30178 AN XY: 73906

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.361

Alfa AF: 0.342 Hom.: 10522

Bravo AF: 0.404

Asia WGS AF: 0.489 AC: 1697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.34
Dann	Benign	0.076

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9287638; hg19: chr2-239694631;