5-179793637-A-C

Variant names:

• chr5-179793637-A-C
• rs730012

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 0.283 in 985,288 control chromosomes in the GnomAD database, including 41,327 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 0.22 (4362 hom., cov: 33)
  • Exomes 𝑓: 0.29 (36965 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.63
• Publications: 118 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 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: 0.218 AC: 33120 AN: 152064 Hom.: 4363 Cov.: 33

Gnomad AFR AF: 0.0829

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.228

GnomAD4 exome AF: 0.295 AC: 245618 AN: 833108 Hom.: 36965 Cov.: 32 AF XY: 0.294 AC XY: 113239 AN XY: 384714

African (AFR) AF: 0.0613 AC: 967 AN: 15786

American (AMR) AF: 0.203 AC: 200 AN: 984

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 1234 AN: 5152

East Asian (EAS) AF: 0.163 AC: 592 AN: 3630

South Asian (SAS) AF: 0.189 AC: 3110 AN: 16460

European-Finnish (FIN) AF: 0.283 AC: 78 AN: 276

Middle Eastern (MID) AF: 0.229 AC: 371 AN: 1620

European-Non Finnish (NFE) AF: 0.304 AC: 231871 AN: 761902

Other (OTH) AF: 0.264 AC: 7195 AN: 27298

GnomAD4 genome AF: 0.218 AC: 33129 AN: 152180 Hom.: 4362 Cov.: 33 AF XY: 0.217 AC XY: 16173 AN XY: 74414

African (AFR) AF: 0.0829 AC: 3443 AN: 41544

American (AMR) AF: 0.179 AC: 2738 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 830 AN: 3470

East Asian (EAS) AF: 0.165 AC: 854 AN: 5176

South Asian (SAS) AF: 0.188 AC: 907 AN: 4826

European-Finnish (FIN) AF: 0.332 AC: 3523 AN: 10598

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20157 AN: 67966

Other (OTH) AF: 0.225 AC: 474 AN: 2104

Alfa AF: 0.264 Hom.: 10342

Bravo AF: 0.200

Asia WGS AF: 0.165 AC: 573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.0040
DANN	Benign	0.70
PhyloP100		-3.6
PromoterAI		-0.042	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Other links and lift over

dbSNP: rs730012; hg19: chr5-179220638;