rs12772169

Variant names:

• chr10-94645572-C-T
• rs12772169

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 0.275 in 152,104 control chromosomes in the GnomAD database, including 6,305 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 0.27 (6305 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163
• Publications: 23 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.435 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: 0.275 AC: 41762 AN: 151986 Hom.: 6296 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.275 AC: 41797 AN: 152104 Hom.: 6305 Cov.: 32 AF XY: 0.278 AC XY: 20687 AN XY: 74368

African (AFR) AF: 0.388 AC: 16104 AN: 41476

American (AMR) AF: 0.199 AC: 3039 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 740 AN: 3462

East Asian (EAS) AF: 0.359 AC: 1854 AN: 5160

South Asian (SAS) AF: 0.450 AC: 2171 AN: 4820

European-Finnish (FIN) AF: 0.234 AC: 2480 AN: 10580

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14641 AN: 68000

Other (OTH) AF: 0.248 AC: 524 AN: 2114

Alfa AF: 0.236 Hom.: 15732

Bravo AF: 0.271

Asia WGS AF: 0.397 AC: 1381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.54
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs12772169; hg19: chr10-96405329;