rs12203952

chr6-62856909-G-Achr6-62856909-G-Cchr6-62856909-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 0.249 in 151,642 control chromosomes in the GnomAD database, including 4,983 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 0.25 (4983 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.402 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: 0.249 AC: 37741 AN: 151522 Hom.: 4970 Cov.: 31

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.249 AC: 37798 AN: 151642 Hom.: 4983 Cov.: 31 AF XY: 0.253 AC XY: 18720 AN XY: 74100

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.255

Alfa AF: 0.123 Hom.: 195

Bravo AF: 0.253

Asia WGS AF: 0.400 AC: 1388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	6.8
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12203952; hg19: chr6-63566814;