rs877282

Variant names:

• chr10-725592-G-A
• rs877282

Your query was ambiguous. Multiple possible variants found:

• chr10-725592-G-A
• chr10-725592-G-C
• chr10-725592-G-T

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 0.126 in 152,192 control chromosomes in the GnomAD database, including 1,470 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 0.13 (1470 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.742
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.173 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: 0.126 AC: 19177 AN: 152074 Hom.: 1469 Cov.: 33

Gnomad AFR AF: 0.0511

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0779

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.126 AC: 19188 AN: 152192 Hom.: 1470 Cov.: 33 AF XY: 0.122 AC XY: 9050 AN XY: 74420

African (AFR) AF: 0.0510 AC: 2120 AN: 41550

American (AMR) AF: 0.164 AC: 2510 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 455 AN: 3468

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5176

South Asian (SAS) AF: 0.0784 AC: 378 AN: 4824

European-Finnish (FIN) AF: 0.120 AC: 1267 AN: 10600

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11971 AN: 67982

Other (OTH) AF: 0.146 AC: 307 AN: 2108

Alfa AF: 0.154 Hom.: 3638

Bravo AF: 0.128

Asia WGS AF: 0.0430 AC: 149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.94
DANN	Benign	0.70
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs877282; hg19: chr10-771532;