10-122902204-T-G

Variant names:

• chr10-122902204-T-G
• rs12354676

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 0.0142 in 152,248 control chromosomes in the GnomAD database, including 31 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 0.014 (31 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.129

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0623 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: 0.0142 AC: 2162 AN: 152130 Hom.: 31 Cov.: 32

Gnomad AFR AF: 0.00323

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0167

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.0680

Gnomad SAS AF: 0.0143

Gnomad FIN AF: 0.00989

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0174

Gnomad OTH AF: 0.00907

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

GnomAD4 genome AF: 0.0142 AC: 2163 AN: 152248 Hom.: 31 Cov.: 32 AF XY: 0.0143 AC XY: 1061 AN XY: 74418

Gnomad4 AFR AF: 0.00322

Gnomad4 AMR AF: 0.0167

Gnomad4 ASJ AF: 0.00202

Gnomad4 EAS AF: 0.0681

Gnomad4 SAS AF: 0.0143

Gnomad4 FIN AF: 0.00989

Gnomad4 NFE AF: 0.0174

Gnomad4 OTH AF: 0.00898

Alfa AF: 0.00709 Hom.: 1

Bravo AF: 0.0149

Asia WGS AF: 0.0320 AC: 111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.4
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12354676; hg19: chr10-124661720;