rs10046055

Variant names:

• chr5-157890009-T-A
• rs10046055

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 0.315 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
• Publications: 3 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 (SAS) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.252 AC: 10466 AN: 41456

American (AMR) AF: 0.340 AC: 5186 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1289 AN: 3464

East Asian (EAS) AF: 0.138 AC: 713 AN: 5164

South Asian (SAS) AF: 0.399 AC: 1924 AN: 4826

European-Finnish (FIN) AF: 0.305 AC: 3220 AN: 10558

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.352 AC: 23910 AN: 67956

Other (OTH) AF: 0.313 AC: 662 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.0
DANN	Benign	0.57
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs10046055; hg19: chr5-157317017;