12-127308069-C-T

Variant names:

• chr12-127308069-C-T
• rs1823172

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 0.169 in 152,130 control chromosomes in the GnomAD database, including 2,993 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 0.17 (2993 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.38
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 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: 0.169 AC: 25633 AN: 152010 Hom.: 2973 Cov.: 33

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.0789

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.169 AC: 25700 AN: 152130 Hom.: 2993 Cov.: 33 AF XY: 0.174 AC XY: 12924 AN XY: 74370

African (AFR) AF: 0.314 AC: 13040 AN: 41484

American (AMR) AF: 0.147 AC: 2249 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 544 AN: 3470

East Asian (EAS) AF: 0.289 AC: 1494 AN: 5170

South Asian (SAS) AF: 0.218 AC: 1053 AN: 4822

European-Finnish (FIN) AF: 0.143 AC: 1510 AN: 10590

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.0790 AC: 5371 AN: 67994

Other (OTH) AF: 0.155 AC: 327 AN: 2112

Alfa AF: 0.113 Hom.: 4775

Bravo AF: 0.176

Asia WGS AF: 0.277 AC: 967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.31
DANN	Benign	0.37
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs1823172; hg19: chr12-127792614;