rs10519957

chr5-127697155-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 0.0578 in 151,822 control chromosomes in the GnomAD database, including 571 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 0.058 (571 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 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: 0.0577 AC: 8754 AN: 151704 Hom.: 570 Cov.: 32

Gnomad AFR AF: 0.0913

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.0906

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.0817

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0106

Gnomad OTH AF: 0.0686

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

GnomAD4 genome AF: 0.0578 AC: 8768 AN: 151822 Hom.: 571 Cov.: 32 AF XY: 0.0608 AC XY: 4510 AN XY: 74194

Gnomad4 AFR AF: 0.0913

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.0906

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.0820

Gnomad4 FIN AF: 0.00104

Gnomad4 NFE AF: 0.0106

Gnomad4 OTH AF: 0.0717

Alfa AF: 0.0330 Hom.: 33

Bravo AF: 0.0703

Asia WGS AF: 0.170 AC: 591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.58
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519957; hg19: chr5-127032847;