rs12665321

Variant names:

• chr6-86059571-C-A
• rs12665321

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 0.235 in 151,528 control chromosomes in the GnomAD database, including 5,117 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 (5117 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.986

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 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: 0.235 AC: 35580 AN: 151412 Hom.: 5117 Cov.: 31

Gnomad AFR AF: 0.0844

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.235 AC: 35578 AN: 151528 Hom.: 5117 Cov.: 31 AF XY: 0.233 AC XY: 17270 AN XY: 73992

Gnomad4 AFR AF: 0.0843

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.227

Alfa AF: 0.277 Hom.: 806

Bravo AF: 0.214

Asia WGS AF: 0.227 AC: 788 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	11
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12665321; hg19: chr6-86769289;