chr1-58584660-A-G

Position:

• chr1-58584660-A-G

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 0.147 in 152,132 control chromosomes in the GnomAD database, including 1,699 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 0.15 (1699 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.17 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: 0.147 AC: 22274 AN: 152014 Hom.: 1698 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0523

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0934

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.147 AC: 22288 AN: 152132 Hom.: 1699 Cov.: 32 AF XY: 0.141 AC XY: 10463 AN XY: 74370

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.0522

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.0934

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.139

Alfa AF: 0.146 Hom.: 856

Bravo AF: 0.148

Asia WGS AF: 0.0900 AC: 313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.5
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6690139; hg19: chr1-59050332; COSMIC: COSV59945409;