rs10411428

Variant names:

• chr19-52104512-C-T
• rs10411428

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.126 AC: 5220 AN: 41526

American (AMR) AF: 0.200 AC: 3054 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 427 AN: 3470

East Asian (EAS) AF: 0.439 AC: 2267 AN: 5162

South Asian (SAS) AF: 0.294 AC: 1419 AN: 4830

European-Finnish (FIN) AF: 0.171 AC: 1806 AN: 10566

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12689 AN: 67982

Other (OTH) AF: 0.188 AC: 397 AN: 2114

Alfa AF: 0.192 Hom.: 5663

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
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs10411428; hg19: chr19-52607765;