rs9287638

Variant names:

• chr2-238785990-C-A
• rs9287638

Your query was ambiguous. Multiple possible variants found:

• chr2-238785990-C-A
• chr2-238785990-C-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 0.402 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
• Publications: 25 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.508 AC: 20948 AN: 41198

American (AMR) AF: 0.414 AC: 6310 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1032 AN: 3464

East Asian (EAS) AF: 0.483 AC: 2475 AN: 5120

South Asian (SAS) AF: 0.486 AC: 2317 AN: 4768

European-Finnish (FIN) AF: 0.427 AC: 4430 AN: 10386

Middle Eastern (MID) AF: 0.308 AC: 90 AN: 292

European-Non Finnish (NFE) AF: 0.327 AC: 22172 AN: 67894

Other (OTH) AF: 0.361 AC: 757 AN: 2096

Alfa AF: 0.351 Hom.: 29581

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
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs9287638; hg19: chr2-239694631;