rs12174208

Variant names:

• chr6-153957249-G-T
• rs12174208

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 0.184 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.118 AC: 4886 AN: 41450

American (AMR) AF: 0.250 AC: 3824 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 782 AN: 3466

East Asian (EAS) AF: 0.335 AC: 1734 AN: 5174

South Asian (SAS) AF: 0.365 AC: 1757 AN: 4812

European-Finnish (FIN) AF: 0.232 AC: 2430 AN: 10496

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11953 AN: 67958

Other (OTH) AF: 0.188 AC: 397 AN: 2110

Alfa AF: 0.176 Hom.: 780

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
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs12174208; hg19: chr6-154278384;