rs2505990

Variant names:

• chr10-43069900-C-A
• rs2505990

Your query was ambiguous. Multiple possible variants found:

• chr10-43069900-C-A
• chr10-43069900-C-G
• chr10-43069900-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 0.809 in 152,096 control chromosomes in the GnomAD database, including 50,593 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 0.81 (50593 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632

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 (AFR) allele frequency at 95% confidence interval = 0.949 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: 0.809 AC: 122893 AN: 151978 Hom.: 50526 Cov.: 32

Gnomad AFR AF: 0.957

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.795

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

GnomAD4 genome AF: 0.809 AC: 123024 AN: 152096 Hom.: 50593 Cov.: 32 AF XY: 0.801 AC XY: 59567 AN XY: 74328

Gnomad4 AFR AF: 0.957

Gnomad4 AMR AF: 0.775

Gnomad4 ASJ AF: 0.712

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.649

Gnomad4 NFE AF: 0.769

Gnomad4 OTH AF: 0.797

Alfa AF: 0.774 Hom.: 6722

Bravo AF: 0.828

Asia WGS AF: 0.732 AC: 2548 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	1.0
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2505990; hg19: chr10-43565348;