chr10-121458867-C-G

Variant names:

• chr10-121458867-C-G
• rs12776781

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 0.31 in 152,074 control chromosomes in the GnomAD database, including 9,068 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 0.31 (9068 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.447 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: 0.310 AC: 47080 AN: 151956 Hom.: 9068 Cov.: 32

Gnomad AFR AF: 0.0910

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.310 AC: 47087 AN: 152074 Hom.: 9068 Cov.: 32 AF XY: 0.312 AC XY: 23185 AN XY: 74338

Gnomad4 AFR AF: 0.0911

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.338

Alfa AF: 0.239 Hom.: 681

Bravo AF: 0.279

Asia WGS AF: 0.359 AC: 1255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.86
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12776781; hg19: chr10-123218381;