rs12455580

Variant names:

• chr18-77926067-T-C
• rs12455580

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 0.511 in 152,106 control chromosomes in the GnomAD database, including 22,113 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 0.51 (22113 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 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: 0.512 AC: 77784 AN: 151988 Hom.: 22123 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.511 AC: 77786 AN: 152106 Hom.: 22113 Cov.: 32 AF XY: 0.517 AC XY: 38427 AN XY: 74376

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.521

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.522

Alfa AF: 0.591 Hom.: 29347

Bravo AF: 0.495

Asia WGS AF: 0.613 AC: 2133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.58
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12455580; hg19: chr18-75638023;