rs10519922

chr5-127094961-T-G

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 0.0446 in 152,320 control chromosomes in the GnomAD database, including 288 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 0.045 (288 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630

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 (SAS) allele frequency at 95% confidence interval = 0.124 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: 0.0445 AC: 6770 AN: 152202 Hom.: 287 Cov.: 33

Gnomad AFR AF: 0.0944

Gnomad AMI AF: 0.0209

Gnomad AMR AF: 0.0273

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.0877

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0195

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0128

Gnomad OTH AF: 0.0339

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

GnomAD4 genome AF: 0.0446 AC: 6786 AN: 152320 Hom.: 288 Cov.: 33 AF XY: 0.0468 AC XY: 3487 AN XY: 74482

Gnomad4 AFR AF: 0.0944

Gnomad4 AMR AF: 0.0274

Gnomad4 ASJ AF: 0.0444

Gnomad4 EAS AF: 0.0877

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.0195

Gnomad4 NFE AF: 0.0128

Gnomad4 OTH AF: 0.0360

Alfa AF: 0.0339 Hom.: 22

Bravo AF: 0.0450

Asia WGS AF: 0.105 AC: 362 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	3.3
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519922; hg19: chr5-126430653;