rs2505780

Variant names:

• chr10-84700413-C-T
• rs2505780

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.473 AC: 19613 AN: 41450

American (AMR) AF: 0.626 AC: 9576 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 2348 AN: 3470

East Asian (EAS) AF: 0.438 AC: 2258 AN: 5156

South Asian (SAS) AF: 0.574 AC: 2766 AN: 4820

European-Finnish (FIN) AF: 0.457 AC: 4824 AN: 10552

Middle Eastern (MID) AF: 0.599 AC: 175 AN: 292

European-Non Finnish (NFE) AF: 0.535 AC: 36347 AN: 67956

Other (OTH) AF: 0.565 AC: 1194 AN: 2114

Alfa AF: 0.539 Hom.: 25645

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
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs2505780; hg19: chr10-86460169;