rs12665468

Variant names:

• chr6-148575480-C-A
• rs12665468

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 0.174 in 152,096 control chromosomes in the GnomAD database, including 2,443 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 0.17 (2443 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 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: 0.174 AC: 26425 AN: 151978 Hom.: 2436 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0943

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.174 AC: 26464 AN: 152096 Hom.: 2443 Cov.: 32 AF XY: 0.171 AC XY: 12721 AN XY: 74344

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.0943

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.190

Alfa AF: 0.166 Hom.: 326

Bravo AF: 0.185

Asia WGS AF: 0.196 AC: 683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.18
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12665468; hg19: chr6-148896616;