rs12675001

Variant names:

• chr8-114107210-G-T
• rs12675001

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 0.336 in 149,700 control chromosomes in the GnomAD database, including 8,753 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 0.34 (8753 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 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: 0.336 AC: 50345 AN: 149620 Hom.: 8753 Cov.: 29

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.336 AC: 50362 AN: 149700 Hom.: 8753 Cov.: 29 AF XY: 0.332 AC XY: 24235 AN XY: 72906

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.325

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.359

Alfa AF: 0.379 Hom.: 16995

Bravo AF: 0.331

Asia WGS AF: 0.304 AC: 1058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.81
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12675001; hg19: chr8-115119439;