rs2842276

Variant names:

• chr10-63063452-G-A
• rs2842276

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 0.767 in 152,108 control chromosomes in the GnomAD database, including 45,297 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 0.77 (45297 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.64
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.848 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: 0.768 AC: 116655 AN: 151990 Hom.: 45287 Cov.: 31

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.767 AC: 116708 AN: 152108 Hom.: 45297 Cov.: 31 AF XY: 0.774 AC XY: 57569 AN XY: 74352

African (AFR) AF: 0.637 AC: 26403 AN: 41448

American (AMR) AF: 0.822 AC: 12557 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2761 AN: 3470

East Asian (EAS) AF: 0.813 AC: 4209 AN: 5176

South Asian (SAS) AF: 0.870 AC: 4197 AN: 4826

European-Finnish (FIN) AF: 0.882 AC: 9345 AN: 10592

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.803 AC: 54606 AN: 67994

Other (OTH) AF: 0.776 AC: 1638 AN: 2112

Alfa AF: 0.795 Hom.: 207206

Bravo AF: 0.757

Asia WGS AF: 0.819 AC: 2850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.3
DANN	Benign	0.34
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs2842276; hg19: chr10-64823212;