2-10436306-C-T

Variant names:

• chr2-10436306-C-T
• rs10929669

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 0.112 in 152,246 control chromosomes in the GnomAD database, including 1,052 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 0.11 (1052 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.733

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.253 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: 0.112 AC: 17042 AN: 152128 Hom.: 1053 Cov.: 34

Gnomad AFR AF: 0.0731

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.0994

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0979

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

GnomAD4 genome AF: 0.112 AC: 17032 AN: 152246 Hom.: 1052 Cov.: 34 AF XY: 0.115 AC XY: 8524 AN XY: 74428

Gnomad4 AFR AF: 0.0731

Gnomad4 AMR AF: 0.0989

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.0959

Alfa AF: 0.116 Hom.: 134

Bravo AF: 0.104

Asia WGS AF: 0.186 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.0
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10929669; hg19: chr2-10576432;