rs10519479

chr5-116714452-C-T

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 0.0556 in 152,078 control chromosomes in the GnomAD database, including 672 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 0.056 (672 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.172 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: 0.0555 AC: 8433 AN: 151960 Hom.: 671 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0248

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0220

Gnomad FIN AF: 0.00642

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00784

Gnomad OTH AF: 0.0507

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

GnomAD4 genome AF: 0.0556 AC: 8463 AN: 152078 Hom.: 672 Cov.: 32 AF XY: 0.0543 AC XY: 4037 AN XY: 74332

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.0248

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0218

Gnomad4 FIN AF: 0.00642

Gnomad4 NFE AF: 0.00784

Gnomad4 OTH AF: 0.0521

Alfa AF: 0.0136 Hom.: 187

Bravo AF: 0.0620

Asia WGS AF: 0.0250 AC: 86 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
Cadd	Benign	11
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519479; hg19: chr5-116050148;