rs12767486

Variant names:

• chr10-84889891-C-T
• rs12767486

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 0.282 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.209 AC: 8670 AN: 41450

American (AMR) AF: 0.310 AC: 4744 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1240 AN: 3466

East Asian (EAS) AF: 0.386 AC: 1992 AN: 5166

South Asian (SAS) AF: 0.297 AC: 1434 AN: 4826

European-Finnish (FIN) AF: 0.292 AC: 3077 AN: 10554

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.304 AC: 20689 AN: 67946

Other (OTH) AF: 0.283 AC: 595 AN: 2106

Alfa AF: 0.299 Hom.: 29365

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
PhyloP100		0.022

Splicing

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

Other links and lift over

dbSNP: rs12767486; hg19: chr10-86649647;