rs1823172

Positions:

• chr12-127308069-C-T

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 0.169 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.0790

Gnomad4 OTH AF: 0.155

Alfa AF: 0.103 Hom.: 1526

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1823172; hg19: chr12-127792614;