rs2039964

Variant names:

• chr10-106494706-G-A
• rs2039964

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 0.307 in 151,886 control chromosomes in the GnomAD database, including 7,510 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 0.31 (7510 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.422 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: 0.307 AC: 46563 AN: 151768 Hom.: 7507 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.307 AC: 46594 AN: 151886 Hom.: 7510 Cov.: 32 AF XY: 0.307 AC XY: 22801 AN XY: 74226

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.268

Alfa AF: 0.304 Hom.: 917

Bravo AF: 0.311

Asia WGS AF: 0.381 AC: 1322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2039964; hg19: chr10-108254464;