rs10519923

Positions:

• chr5-127095083-G-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 0.0187 in 152,254 control chromosomes in the GnomAD database, including 69 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 0.019 (69 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.850

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.106 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: 0.0187 AC: 2849 AN: 152136 Hom.: 69 Cov.: 33

Gnomad AFR AF: 0.0120

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0137

Gnomad ASJ AF: 0.0432

Gnomad EAS AF: 0.0616

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0193

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0124

Gnomad OTH AF: 0.0172

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

GnomAD4 genome AF: 0.0187 AC: 2845 AN: 152254 Hom.: 69 Cov.: 33 AF XY: 0.0207 AC XY: 1542 AN XY: 74444

Gnomad4 AFR AF: 0.0119

Gnomad4 AMR AF: 0.0137

Gnomad4 ASJ AF: 0.0432

Gnomad4 EAS AF: 0.0616

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0193

Gnomad4 NFE AF: 0.0124

Gnomad4 OTH AF: 0.0166

Alfa AF: 0.0116 Hom.: 3

Bravo AF: 0.0157

Asia WGS AF: 0.0600 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.0
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519923; hg19: chr5-126430775;