rs12216336

chr6-32999964-G-Cchr6-32999964-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 0.321 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.365

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12216336; hg19: chr6-32967741;