5-106645130-C-G

Variant names:

• chr5-106645130-C-G
• rs12517578

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 0.254 in 151,746 control chromosomes in the GnomAD database, including 4,992 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 0.25 (4992 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38538 AN: 151628 Hom.: 4969 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.254 AC: 38619 AN: 151746 Hom.: 4992 Cov.: 32 AF XY: 0.257 AC XY: 19080 AN XY: 74146

African (AFR) AF: 0.266 AC: 11036 AN: 41436

American (AMR) AF: 0.257 AC: 3917 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 876 AN: 3470

East Asian (EAS) AF: 0.428 AC: 2204 AN: 5148

South Asian (SAS) AF: 0.344 AC: 1657 AN: 4822

European-Finnish (FIN) AF: 0.229 AC: 2418 AN: 10540

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.230 AC: 15594 AN: 67810

Other (OTH) AF: 0.285 AC: 600 AN: 2104

Alfa AF: 0.112 Hom.: 138

Bravo AF: 0.257

Asia WGS AF: 0.391 AC: 1348 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.7
DANN	Benign	0.72
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs12517578; hg19: chr5-105980831; COSMIC: COSV50462502;