rs2842275

Variant names:

• chr10-63064211-C-G
• rs2842275

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 0.925 in 152,248 control chromosomes in the GnomAD database, including 65,307 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 0.93 (65307 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.925 AC: 140736 AN: 152130 Hom.: 65263 Cov.: 32

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.995

Gnomad AMR AF: 0.954

Gnomad ASJ AF: 0.933

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.989

Gnomad FIN AF: 0.965

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.939

Gnomad OTH AF: 0.943

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

GnomAD4 genome AF: 0.925 AC: 140838 AN: 152248 Hom.: 65307 Cov.: 32 AF XY: 0.928 AC XY: 69069 AN XY: 74440

Gnomad4 AFR AF: 0.861

Gnomad4 AMR AF: 0.954

Gnomad4 ASJ AF: 0.933

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.989

Gnomad4 FIN AF: 0.965

Gnomad4 NFE AF: 0.939

Gnomad4 OTH AF: 0.944

Alfa AF: 0.920 Hom.: 8010

Bravo AF: 0.920

Asia WGS AF: 0.985 AC: 3425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.44
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2842275; hg19: chr10-64823971;