rs10193067

Positions:

• chr2-52463275-A-C

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 0.0849 in 152,220 control chromosomes in the GnomAD database, including 773 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 0.085 (773 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0849 AC: 12912 AN: 152102 Hom.: 771 Cov.: 33

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0495

Gnomad EAS AF: 0.0763

Gnomad SAS AF: 0.0428

Gnomad FIN AF: 0.0579

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0386

Gnomad OTH AF: 0.0678

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

GnomAD4 genome AF: 0.0849 AC: 12928 AN: 152220 Hom.: 773 Cov.: 33 AF XY: 0.0847 AC XY: 6305 AN XY: 74414

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.0495

Gnomad4 EAS AF: 0.0757

Gnomad4 SAS AF: 0.0429

Gnomad4 FIN AF: 0.0579

Gnomad4 NFE AF: 0.0386

Gnomad4 OTH AF: 0.0709

Alfa AF: 0.0487 Hom.: 389

Bravo AF: 0.0972

Asia WGS AF: 0.0660 AC: 231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.1
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10193067; hg19: chr2-52690413;