rs10411428

Positions:

• chr19-52104512-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 0.181 in 152,132 control chromosomes in the GnomAD database, including 2,886 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 0.18 (2886 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117

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 = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27465 AN: 152014 Hom.: 2881 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.181 AC: 27496 AN: 152132 Hom.: 2886 Cov.: 32 AF XY: 0.185 AC XY: 13750 AN XY: 74374

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.188

Alfa AF: 0.193 Hom.: 1698

Bravo AF: 0.179

Asia WGS AF: 0.353 AC: 1225 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.0
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10411428; hg19: chr19-52607765;