1-58575047-T-C

Position:

• chr1-58575047-T-C

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 0.246 in 152,088 control chromosomes in the GnomAD database, including 6,218 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 (6218 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193

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 (AFR) allele frequency at 95% confidence interval = 0.466 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: 0.246 AC: 37372 AN: 151970 Hom.: 6196 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.246 AC: 37424 AN: 152088 Hom.: 6218 Cov.: 32 AF XY: 0.239 AC XY: 17756 AN XY: 74352

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.224

Alfa AF: 0.175 Hom.: 3154

Bravo AF: 0.258

Asia WGS AF: 0.164 AC: 571 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	6.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs232840; hg19: chr1-59040719;