rs10500264

chr19-33259408-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 0.144 in 152,022 control chromosomes in the GnomAD database, including 1,759 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 0.14 (1759 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.229 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: 0.144 AC: 21899 AN: 151904 Hom.: 1755 Cov.: 32

Gnomad AFR AF: 0.0864

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.0684

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.144 AC: 21907 AN: 152022 Hom.: 1759 Cov.: 32 AF XY: 0.145 AC XY: 10757 AN XY: 74306

Gnomad4 AFR AF: 0.0864

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.0682

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.164

Alfa AF: 0.170 Hom.: 5337

Bravo AF: 0.135

Asia WGS AF: 0.136 AC: 474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	6.0
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10500264; hg19: chr19-33750314;