rs12201301

Variant names:

• chr6-31039780-G-A
• rs12201301

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0266 in 152,214 control chromosomes in the GnomAD database, including 72 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 0.027 (72 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.690
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0266 (4045/152214) while in subpopulation NFE AF = 0.0295 (2003/68004). AF 95% confidence interval is 0.0284. There are 72 homozygotes in GnomAd4. There are 2006 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 72 gene

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0266 AC: 4044 AN: 152096 Hom.: 72 Cov.: 32

Gnomad AFR AF: 0.0211

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0168

Gnomad ASJ AF: 0.0685

Gnomad EAS AF: 0.0197

Gnomad SAS AF: 0.0135

Gnomad FIN AF: 0.0386

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0295

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0266 AC: 4045 AN: 152214 Hom.: 72 Cov.: 32 AF XY: 0.0270 AC XY: 2006 AN XY: 74398

African (AFR) AF: 0.0212 AC: 879 AN: 41542

American (AMR) AF: 0.0167 AC: 256 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0685 AC: 238 AN: 3472

East Asian (EAS) AF: 0.0197 AC: 102 AN: 5172

South Asian (SAS) AF: 0.0133 AC: 64 AN: 4818

European-Finnish (FIN) AF: 0.0386 AC: 409 AN: 10600

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0295 AC: 2003 AN: 68004

Other (OTH) AF: 0.0298 AC: 63 AN: 2114

Alfa AF: 0.0276 Hom.: 146

Bravo AF: 0.0266

Asia WGS AF: 0.0100 AC: 35 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.70
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs12201301; hg19: chr6-31007557;