1-58575047-T-C

Variant names:

• chr1-58575047-T-C
• rs232840

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 0.246 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
• Publications: 8 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 (AFR) allele frequency at 95% confidence interval = 0.466 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: 0.246 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

African (AFR) AF: 0.472 AC: 19552 AN: 41444

American (AMR) AF: 0.154 AC: 2353 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 670 AN: 3472

East Asian (EAS) AF: 0.127 AC: 657 AN: 5184

South Asian (SAS) AF: 0.163 AC: 787 AN: 4824

European-Finnish (FIN) AF: 0.125 AC: 1328 AN: 10586

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.167 AC: 11344 AN: 67980

Other (OTH) AF: 0.224 AC: 474 AN: 2114

Alfa AF: 0.186 Hom.: 4735

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
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs232840; hg19: chr1-59040719;