rs10490009

Variant names:

• chr2-233874269-T-C
• rs10490009

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 0.0644 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.176 AC: 7313 AN: 41516

American (AMR) AF: 0.0545 AC: 833 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00230 AC: 8 AN: 3472

East Asian (EAS) AF: 0.204 AC: 1056 AN: 5178

South Asian (SAS) AF: 0.0284 AC: 137 AN: 4828

European-Finnish (FIN) AF: 0.00508 AC: 54 AN: 10624

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00429 AC: 292 AN: 68028

Other (OTH) AF: 0.0530 AC: 112 AN: 2112

Alfa AF: 0.0292 Hom.: 564

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
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs10490009; hg19: chr2-234782915; COSMIC: COSV107166583;