rs730012

Variant names:

• chr5-179793637-A-C
• rs730012

Your query was ambiguous. Multiple possible variants found:

• chr5-179793637-A-C
• chr5-179793637-A-G
• chr5-179793637-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;