rs730012

chr5-179793637-A-Cchr5-179793637-A-Gchr5-179793637-A-T

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 0.283 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR exome AF: 0.0613

Gnomad4 AMR exome AF: 0.203

Gnomad4 ASJ exome AF: 0.240

Gnomad4 EAS exome AF: 0.163

Gnomad4 SAS exome AF: 0.189

Gnomad4 FIN exome AF: 0.283

Gnomad4 NFE exome AF: 0.304

Gnomad4 OTH exome AF: 0.264

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

Gnomad4 AFR AF: 0.0829

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.225

Alfa AF: 0.265 Hom.: 7152

Bravo AF: 0.200

Asia WGS AF: 0.165 AC: 573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.0040
Dann	Benign	0.70
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

Publications

LitVar

Other links and lift over

dbSNP: rs730012; hg19: chr5-179220638;