rs10520297

Variant names:

• chr2-82154227-C-T
• rs10520297

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 0.194 in 152,086 control chromosomes in the GnomAD database, including 3,316 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 0.19 (3316 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 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: 0.194 AC: 29414 AN: 151968 Hom.: 3309 Cov.: 32

Gnomad AFR AF: 0.0813

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.194 AC: 29442 AN: 152086 Hom.: 3316 Cov.: 32 AF XY: 0.194 AC XY: 14451 AN XY: 74334

African (AFR) AF: 0.0815 AC: 3384 AN: 41522

American (AMR) AF: 0.220 AC: 3363 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 796 AN: 3472

East Asian (EAS) AF: 0.290 AC: 1498 AN: 5166

South Asian (SAS) AF: 0.132 AC: 636 AN: 4820

European-Finnish (FIN) AF: 0.278 AC: 2938 AN: 10556

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16143 AN: 67960

Other (OTH) AF: 0.201 AC: 424 AN: 2110

Alfa AF: 0.217 Hom.: 662

Bravo AF: 0.190

Asia WGS AF: 0.165 AC: 571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.20
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs10520297; hg19: chr2-82381351;