chr2-170099261-G-A

Variant names:

• chr2-170099261-G-A
• rs10497352

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;