rs12141375

Variant names:

• chr1-203212234-C-A
• rs12141375

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 0.19 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
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0657 AC: 2732 AN: 41566

American (AMR) AF: 0.264 AC: 4033 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 766 AN: 3472

East Asian (EAS) AF: 0.571 AC: 2948 AN: 5160

South Asian (SAS) AF: 0.443 AC: 2135 AN: 4824

European-Finnish (FIN) AF: 0.185 AC: 1960 AN: 10594

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13694 AN: 67982

Other (OTH) AF: 0.215 AC: 455 AN: 2112

Alfa AF: 0.204 Hom.: 11073

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
PhyloP100		0.0080

Splicing

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

Other links and lift over

dbSNP: rs12141375; hg19: chr1-203181362;