rs12661352

Variant names:

• chr6-32777750-G-T
• rs12661352

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 0.0585 in 152,294 control chromosomes in the GnomAD database, including 342 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 0.058 (342 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0881 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: 0.0586 AC: 8914 AN: 152176 Hom.: 341 Cov.: 32

Gnomad AFR AF: 0.0168

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0783

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.0231

Gnomad SAS AF: 0.0954

Gnomad FIN AF: 0.0888

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0725

Gnomad OTH AF: 0.0738

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

GnomAD4 genome AF: 0.0585 AC: 8909 AN: 152294 Hom.: 342 Cov.: 32 AF XY: 0.0603 AC XY: 4487 AN XY: 74468

Gnomad4 AFR AF: 0.0169

Gnomad4 AMR AF: 0.0782

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.0231

Gnomad4 SAS AF: 0.0953

Gnomad4 FIN AF: 0.0888

Gnomad4 NFE AF: 0.0726

Gnomad4 OTH AF: 0.0725

Alfa AF: 0.0618 Hom.: 83

Bravo AF: 0.0531

Asia WGS AF: 0.0610 AC: 215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.9
DANN	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12661352; hg19: chr6-32745527;