rs1158058

Variant names:

• chr6-71016836-A-T
• rs1158058

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 0.278 in 152,056 control chromosomes in the GnomAD database, including 6,338 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 0.28 (6338 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.333 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: 0.278 AC: 42206 AN: 151938 Hom.: 6332 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.278 AC: 42237 AN: 152056 Hom.: 6338 Cov.: 32 AF XY: 0.275 AC XY: 20425 AN XY: 74318

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.271

Alfa AF: 0.313 Hom.: 964

Bravo AF: 0.264

Asia WGS AF: 0.0860 AC: 301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.0
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1158058; hg19: chr6-71726539;