rs12767486

Variant names:

• chr10-84889891-C-T
• rs12767486

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 0.282 in 151,998 control chromosomes in the GnomAD database, including 6,202 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 0.28 (6202 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.371 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: 0.282 AC: 42774 AN: 151880 Hom.: 6197 Cov.: 31

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.282 AC: 42806 AN: 151998 Hom.: 6202 Cov.: 31 AF XY: 0.279 AC XY: 20744 AN XY: 74272

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.283

Alfa AF: 0.304 Hom.: 14619

Bravo AF: 0.283

Asia WGS AF: 0.335 AC: 1167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12767486; hg19: chr10-86649647;