rs12174208

chr6-153957249-G-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 0.184 in 151,944 control chromosomes in the GnomAD database, including 2,800 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 0.18 (2800 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28015 AN: 151826 Hom.: 2799 Cov.: 33

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.184 AC: 28013 AN: 151944 Hom.: 2800 Cov.: 33 AF XY: 0.194 AC XY: 14391 AN XY: 74236

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.335

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.188

Alfa AF: 0.177 Hom.: 741

Bravo AF: 0.175

Asia WGS AF: 0.363 AC: 1261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.96
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12174208; hg19: chr6-154278384;