rs12143917

Variant names:

• chr1-103891362-G-A
• rs12143917

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.277 AC: 11449 AN: 41394

American (AMR) AF: 0.393 AC: 6000 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1114 AN: 3462

East Asian (EAS) AF: 0.173 AC: 894 AN: 5156

South Asian (SAS) AF: 0.254 AC: 1222 AN: 4808

European-Finnish (FIN) AF: 0.303 AC: 3181 AN: 10506

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26141 AN: 67940

Other (OTH) AF: 0.360 AC: 758 AN: 2106

Alfa AF: 0.369 Hom.: 8826

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
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs12143917; hg19: chr1-104433984;