rs12206002

Variant names:

• chr6-145218331-T-C
• rs12206002

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 0.207 in 152,136 control chromosomes in the GnomAD database, including 3,778 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 0.21 (3778 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.598

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.297 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: 0.207 AC: 31427 AN: 152018 Hom.: 3778 Cov.: 32

Gnomad AFR AF: 0.0789

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.292

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.207 AC: 31423 AN: 152136 Hom.: 3778 Cov.: 32 AF XY: 0.207 AC XY: 15361 AN XY: 74354

Gnomad4 AFR AF: 0.0788

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.224

Alfa AF: 0.253 Hom.: 10188

Bravo AF: 0.207

Asia WGS AF: 0.184 AC: 639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12206002; hg19: chr6-145539467;