chr6-107696467-A-G

Variant names:

• chr6-107696467-A-G
• rs12525668

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;