rs12655480

Positions:

• chr5-178853270-C-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;