rs2505989

Variant names:

• chr10-43068003-G-C
• rs2505989

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 0.326 in 152,158 control chromosomes in the GnomAD database, including 8,753 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 0.33 (8753 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 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: 0.326 AC: 49596 AN: 152040 Hom.: 8746 Cov.: 33

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.0811

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.326 AC: 49618 AN: 152158 Hom.: 8753 Cov.: 33 AF XY: 0.325 AC XY: 24155 AN XY: 74378

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.0811

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.295

Alfa AF: 0.351 Hom.: 1210

Bravo AF: 0.319

Asia WGS AF: 0.204 AC: 712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.7
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2505989; hg19: chr10-43563451;