10-121458867-C-G

Variant names:

• chr10-121458867-C-G
• rs12776781

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 0.31 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0911 AC: 3780 AN: 41494

American (AMR) AF: 0.238 AC: 3630 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1360 AN: 3470

East Asian (EAS) AF: 0.250 AC: 1291 AN: 5162

South Asian (SAS) AF: 0.463 AC: 2228 AN: 4816

European-Finnish (FIN) AF: 0.471 AC: 4973 AN: 10552

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28627 AN: 67976

Other (OTH) AF: 0.338 AC: 715 AN: 2114

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
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs12776781; hg19: chr10-123218381;