rs10046055

Variant names:

• chr5-157890009-T-A
• rs10046055

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 0.315 in 152,010 control chromosomes in the GnomAD database, including 7,828 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 0.32 (7828 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170

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 (SAS) allele frequency at 95% confidence interval = 0.384 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: 0.316 AC: 47928 AN: 151892 Hom.: 7826 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.315 AC: 47938 AN: 152010 Hom.: 7828 Cov.: 32 AF XY: 0.315 AC XY: 23402 AN XY: 74276

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.313

Alfa AF: 0.327 Hom.: 1023

Bravo AF: 0.311

Asia WGS AF: 0.289 AC: 1006 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	3.0
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10046055; hg19: chr5-157317017;