rs12757998

Variant names:

• chr1-182569343-C-T
• rs12757998

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 0.234 in 151,410 control chromosomes in the GnomAD database, including 4,706 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 0.23 (4706 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.294 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: 0.234 AC: 35404 AN: 151292 Hom.: 4703 Cov.: 28

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.00483

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.234 AC: 35408 AN: 151410 Hom.: 4706 Cov.: 28 AF XY: 0.234 AC XY: 17317 AN XY: 73920

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.00484

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.227

Alfa AF: 0.273 Hom.: 2595

Bravo AF: 0.219

Asia WGS AF: 0.0950 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
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: rs12757998; hg19: chr1-182538478;