rs10058824

chr5-175306905-G-A

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 0.06 in 152,006 control chromosomes in the GnomAD database, including 356 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 0.060 (356 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.163 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: 0.0601 AC: 9121 AN: 151888 Hom.: 354 Cov.: 33

Gnomad AFR AF: 0.0963

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.0289

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.0574

Gnomad FIN AF: 0.0411

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0408

Gnomad OTH AF: 0.0503

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

GnomAD4 genome AF: 0.0600 AC: 9124 AN: 152006 Hom.: 356 Cov.: 33 AF XY: 0.0591 AC XY: 4388 AN XY: 74292

Gnomad4 AFR AF: 0.0962

Gnomad4 AMR AF: 0.0288

Gnomad4 ASJ AF: 0.0403

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.0574

Gnomad4 FIN AF: 0.0411

Gnomad4 NFE AF: 0.0408

Gnomad4 OTH AF: 0.0502

Alfa AF: 0.0547 Hom.: 43

Bravo AF: 0.0605

Asia WGS AF: 0.129 AC: 448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.0
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10058824; hg19: chr5-174733908; COSMIC: COSV64602690;