rs12216336

Variant names:

• chr6-32999964-G-C
• rs12216336

Your query was ambiguous. Multiple possible variants found:

• chr6-32999964-G-C
• chr6-32999964-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 0.321 in 152,092 control chromosomes in the GnomAD database, including 8,364 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 0.32 (8364 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.44 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: 0.321 AC: 48766 AN: 151972 Hom.: 8363 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.321 AC: 48807 AN: 152092 Hom.: 8364 Cov.: 32 AF XY: 0.322 AC XY: 23933 AN XY: 74334

African (AFR) AF: 0.244 AC: 10102 AN: 41470

American (AMR) AF: 0.449 AC: 6863 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1745 AN: 3470

East Asian (EAS) AF: 0.324 AC: 1679 AN: 5176

South Asian (SAS) AF: 0.445 AC: 2142 AN: 4818

European-Finnish (FIN) AF: 0.245 AC: 2590 AN: 10562

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22595 AN: 67988

Other (OTH) AF: 0.365 AC: 772 AN: 2114

Alfa AF: 0.320 Hom.: 4466

Bravo AF: 0.334

Asia WGS AF: 0.403 AC: 1401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.30
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs12216336; hg19: chr6-32967741;