rs10490009

Positions:

• chr2-233874269-T-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 0.0644 in 152,262 control chromosomes in the GnomAD database, including 760 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 0.064 (760 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.552

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0642 AC: 9775 AN: 152144 Hom.: 756 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0546

Gnomad ASJ AF: 0.00230

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.0284

Gnomad FIN AF: 0.00508

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00429

Gnomad OTH AF: 0.0536

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

GnomAD4 genome AF: 0.0644 AC: 9810 AN: 152262 Hom.: 760 Cov.: 32 AF XY: 0.0643 AC XY: 4787 AN XY: 74456

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.0545

Gnomad4 ASJ AF: 0.00230

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.0284

Gnomad4 FIN AF: 0.00508

Gnomad4 NFE AF: 0.00429

Gnomad4 OTH AF: 0.0530

Alfa AF: 0.0246 Hom.: 77

Bravo AF: 0.0718

Asia WGS AF: 0.124 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.7
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490009; hg19: chr2-234782915;