rs12143917

Variant names:

• chr1-103891362-G-A
• rs12143917

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 0.337 in 151,830 control chromosomes in the GnomAD database, including 8,995 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 (8995 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

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 (AMR) allele frequency at 95% confidence interval = 0.385 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: 0.337 AC: 51167 AN: 151710 Hom.: 8982 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.337 AC: 51213 AN: 151830 Hom.: 8995 Cov.: 32 AF XY: 0.332 AC XY: 24615 AN XY: 74184

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.360

Alfa AF: 0.368 Hom.: 7398

Bravo AF: 0.342

Asia WGS AF: 0.238 AC: 828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12143917; hg19: chr1-104433984;