rs12525668

Positions:

• chr6-107696467-A-G

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 0.0681 in 152,306 control chromosomes in the GnomAD database, including 492 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 0.068 (492 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.15 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: 0.0681 AC: 10360 AN: 152188 Hom.: 488 Cov.: 32

Gnomad AFR AF: 0.0168

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.0818

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.0764

Gnomad FIN AF: 0.0912

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0725

Gnomad OTH AF: 0.0712

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

GnomAD4 genome AF: 0.0681 AC: 10375 AN: 152306 Hom.: 492 Cov.: 32 AF XY: 0.0698 AC XY: 5199 AN XY: 74478

Gnomad4 AFR AF: 0.0169

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.0818

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.0771

Gnomad4 FIN AF: 0.0912

Gnomad4 NFE AF: 0.0725

Gnomad4 OTH AF: 0.0714

Alfa AF: 0.0772 Hom.: 813

Bravo AF: 0.0751

Asia WGS AF: 0.0930 AC: 324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12525668; hg19: chr6-108017671;