rs12755606

Variant names:

• chr1-159700546-C-G
• rs12755606

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 0.237 in 152,150 control chromosomes in the GnomAD database, including 5,290 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 0.24 (5290 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 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: 0.237 AC: 36034 AN: 152032 Hom.: 5289 Cov.: 32

Gnomad AFR AF: 0.0718

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.0611

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.237 AC: 36051 AN: 152150 Hom.: 5290 Cov.: 32 AF XY: 0.239 AC XY: 17795 AN XY: 74376

Gnomad4 AFR AF: 0.0716

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.0611

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.252

Alfa AF: 0.278 Hom.: 819

Bravo AF: 0.229

Asia WGS AF: 0.161 AC: 563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12755606; hg19: chr1-159670336;