rs12141375

Variant names:

• chr1-203212234-C-A
• rs12141375

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 0.19 in 152,200 control chromosomes in the GnomAD database, including 3,650 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 0.19 (3650 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800

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 (EAS) allele frequency at 95% confidence interval = 0.554 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: 0.190 AC: 28895 AN: 152082 Hom.: 3639 Cov.: 33

Gnomad AFR AF: 0.0657

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.190 AC: 28922 AN: 152200 Hom.: 3650 Cov.: 33 AF XY: 0.198 AC XY: 14750 AN XY: 74410

Gnomad4 AFR AF: 0.0657

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.215

Alfa AF: 0.212 Hom.: 7512

Bravo AF: 0.186

Asia WGS AF: 0.454 AC: 1577 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	1.4
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12141375; hg19: chr1-203181362;