rs12667481

Variant names:

• chr7-107718939-A-G
• rs12667481

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 0.176 in 151,990 control chromosomes in the GnomAD database, including 2,862 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 0.18 (2862 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.776

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.364 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: 0.176 AC: 26732 AN: 151872 Hom.: 2861 Cov.: 31

Gnomad AFR AF: 0.0451

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.176 AC: 26725 AN: 151990 Hom.: 2862 Cov.: 31 AF XY: 0.179 AC XY: 13259 AN XY: 74262

Gnomad4 AFR AF: 0.0450

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.178

Alfa AF: 0.213 Hom.: 4665

Bravo AF: 0.167

Asia WGS AF: 0.273 AC: 950 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12667481; hg19: chr7-107359384;