rs2569360

Variant names:

• chr10-76828987-G-C
• rs2569360

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 0.375 in 151,876 control chromosomes in the GnomAD database, including 11,289 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 0.37 (11289 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 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: 0.375 AC: 56909 AN: 151756 Hom.: 11285 Cov.: 31

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.375 AC: 56921 AN: 151876 Hom.: 11289 Cov.: 31 AF XY: 0.372 AC XY: 27614 AN XY: 74214

African (AFR) AF: 0.232 AC: 9620 AN: 41432

American (AMR) AF: 0.386 AC: 5884 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1746 AN: 3468

East Asian (EAS) AF: 0.386 AC: 1983 AN: 5140

South Asian (SAS) AF: 0.433 AC: 2084 AN: 4816

European-Finnish (FIN) AF: 0.404 AC: 4248 AN: 10522

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29868 AN: 67954

Other (OTH) AF: 0.419 AC: 882 AN: 2106

Alfa AF: 0.394 Hom.: 1509

Bravo AF: 0.371

Asia WGS AF: 0.385 AC: 1342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.8
DANN	Benign	0.71
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs2569360; hg19: chr10-78588745;