rs667472

Variant names:

• chr12-5104987-T-A
• rs667472

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 0.202 in 152,148 control chromosomes in the GnomAD database, including 3,146 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 0.20 (3146 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.232 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: 0.202 AC: 30739 AN: 152030 Hom.: 3140 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.202 AC: 30772 AN: 152148 Hom.: 3146 Cov.: 32 AF XY: 0.202 AC XY: 15058 AN XY: 74398

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.198

Alfa AF: 0.197 Hom.: 386

Bravo AF: 0.205

Asia WGS AF: 0.196 AC: 680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	6.5
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs667472; hg19: chr12-5214153;