rs12655480

Variant names:

• chr5-178853270-C-G
• rs12655480

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.523 AC: 21671 AN: 41418

American (AMR) AF: 0.501 AC: 7646 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1887 AN: 3468

East Asian (EAS) AF: 0.241 AC: 1248 AN: 5182

South Asian (SAS) AF: 0.374 AC: 1801 AN: 4818

European-Finnish (FIN) AF: 0.610 AC: 6407 AN: 10496

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43522 AN: 67964

Other (OTH) AF: 0.555 AC: 1173 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.32
DANN	Benign	0.42
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs12655480; hg19: chr5-178280271;