rs12665468

Positions:

• chr6-148575480-C-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;