rs2505999

Positions:

• chr10-43075999-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 0.347 in 152,104 control chromosomes in the GnomAD database, including 9,591 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 0.35 (9591 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52752 AN: 151986 Hom.: 9569 Cov.: 33

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.347 AC: 52799 AN: 152104 Hom.: 9591 Cov.: 33 AF XY: 0.349 AC XY: 25925 AN XY: 74350

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.355

Alfa AF: 0.383 Hom.: 13641

Bravo AF: 0.346

Asia WGS AF: 0.355 AC: 1234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.4
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2505999; hg19: chr10-43571447;