rs12203952

Variant names:

• chr6-62856909-G-A
• rs12203952

Your query was ambiguous. Multiple possible variants found:

• chr6-62856909-G-A
• chr6-62856909-G-C
• chr6-62856909-G-T

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 0.249 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
• Publications: 2 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.177 AC: 7309 AN: 41398

American (AMR) AF: 0.321 AC: 4883 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 904 AN: 3460

East Asian (EAS) AF: 0.319 AC: 1635 AN: 5118

South Asian (SAS) AF: 0.418 AC: 2007 AN: 4806

European-Finnish (FIN) AF: 0.212 AC: 2233 AN: 10556

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18057 AN: 67774

Other (OTH) AF: 0.255 AC: 538 AN: 2108

Alfa AF: 0.126 Hom.: 208

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
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs12203952; hg19: chr6-63566814;