rs12216101

Variant names:

• chr6-13560810-T-G
• rs12216101

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 0.232 in 152,196 control chromosomes in the GnomAD database, including 4,750 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 0.23 (4750 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.298 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: 0.233 AC: 35377 AN: 152078 Hom.: 4749 Cov.: 33

Gnomad AFR AF: 0.0946

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.232 AC: 35369 AN: 152196 Hom.: 4750 Cov.: 33 AF XY: 0.230 AC XY: 17081 AN XY: 74416

African (AFR) AF: 0.0943 AC: 3920 AN: 41556

American (AMR) AF: 0.245 AC: 3744 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1040 AN: 3470

East Asian (EAS) AF: 0.247 AC: 1277 AN: 5176

South Asian (SAS) AF: 0.261 AC: 1258 AN: 4828

European-Finnish (FIN) AF: 0.243 AC: 2572 AN: 10582

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20483 AN: 67980

Other (OTH) AF: 0.264 AC: 557 AN: 2112

Alfa AF: 0.279 Hom.: 24187

Bravo AF: 0.225

Asia WGS AF: 0.215 AC: 749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.9
DANN	Benign	0.52
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs12216101; hg19: chr6-13561042;