2-52463275-A-C

Variant names:

• chr2-52463275-A-C
• rs10193067

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 0.0849 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.161 AC: 6687 AN: 41538

American (AMR) AF: 0.134 AC: 2048 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0495 AC: 172 AN: 3472

East Asian (EAS) AF: 0.0757 AC: 392 AN: 5178

South Asian (SAS) AF: 0.0429 AC: 207 AN: 4828

European-Finnish (FIN) AF: 0.0579 AC: 614 AN: 10600

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0386 AC: 2623 AN: 68000

Other (OTH) AF: 0.0709 AC: 150 AN: 2116

Alfa AF: 0.0535 Hom.: 584

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
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs10193067; hg19: chr2-52690413;