chr2-117448358-C-A

Variant names:

• chr2-117448358-C-A
• rs10496540

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 0.12 in 151,938 control chromosomes in the GnomAD database, including 2,223 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 0.12 (2223 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.325

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.306 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: 0.120 AC: 18162 AN: 151820 Hom.: 2201 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.00926

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0413

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0334

Gnomad OTH AF: 0.0964

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

GnomAD4 genome AF: 0.120 AC: 18225 AN: 151938 Hom.: 2223 Cov.: 32 AF XY: 0.119 AC XY: 8826 AN XY: 74272

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.0519

Gnomad4 EAS AF: 0.00909

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0413

Gnomad4 NFE AF: 0.0334

Gnomad4 OTH AF: 0.0954

Alfa AF: 0.0905 Hom.: 169

Bravo AF: 0.131

Asia WGS AF: 0.0860 AC: 298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496540; hg19: chr2-118205934;