rs2505780

Variant names:

• chr10-84700413-C-T
• rs2505780

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 0.523 in 152,012 control chromosomes in the GnomAD database, including 21,137 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 0.52 (21137 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.616 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: 0.523 AC: 79421 AN: 151894 Hom.: 21108 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.523 AC: 79506 AN: 152012 Hom.: 21137 Cov.: 32 AF XY: 0.524 AC XY: 38915 AN XY: 74296

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.677

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.565

Alfa AF: 0.546 Hom.: 18354

Bravo AF: 0.533

Asia WGS AF: 0.561 AC: 1950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.1
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2505780; hg19: chr10-86460169;