rs10497352

Positions:

• chr2-170099261-G-A
• chr2-170099261-G-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 0.102 in 152,158 control chromosomes in the GnomAD database, including 1,137 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 0.10 (1137 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.184 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: 0.102 AC: 15518 AN: 152040 Hom.: 1133 Cov.: 32

Gnomad AFR AF: 0.0414

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.0522

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.0845

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0934

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

GnomAD4 genome AF: 0.102 AC: 15540 AN: 152158 Hom.: 1137 Cov.: 32 AF XY: 0.106 AC XY: 7859 AN XY: 74358

Gnomad4 AFR AF: 0.0415

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.0522

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.0844

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.0924

Alfa AF: 0.110 Hom.: 467

Bravo AF: 0.100

Asia WGS AF: 0.0380 AC: 132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497352; hg19: chr2-170955771;