rs12455580

chr18-77926067-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;