rs12655480

Variant names:

• chr5-178853270-C-G
• rs12655480

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 0.567 in 151,926 control chromosomes in the GnomAD database, including 25,306 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 0.57 (25306 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.635 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: 0.568 AC: 86152 AN: 151808 Hom.: 25302 Cov.: 32

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.567 AC: 86194 AN: 151926 Hom.: 25306 Cov.: 32 AF XY: 0.559 AC XY: 41491 AN XY: 74234

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.555

Alfa AF: 0.600 Hom.: 3442

Bravo AF: 0.556

Asia WGS AF: 0.311 AC: 1085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.32
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12655480; hg19: chr5-178280271;