chr2-238785990-C-A

Variant names:

• chr2-238785990-C-A
• rs9287638

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 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

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;