rs10518275

chr19-33359935-A-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 0.155 in 152,212 control chromosomes in the GnomAD database, including 2,178 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 0.16 (2178 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.249 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: 0.155 AC: 23638 AN: 152094 Hom.: 2170 Cov.: 33

Gnomad AFR AF: 0.0842

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0546

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.155 AC: 23664 AN: 152212 Hom.: 2178 Cov.: 33 AF XY: 0.155 AC XY: 11555 AN XY: 74420

Gnomad4 AFR AF: 0.0841

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.0557

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.184

Alfa AF: 0.175 Hom.: 1441

Bravo AF: 0.160

Asia WGS AF: 0.0410 AC: 144 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	6.3
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518275; hg19: chr19-33850841;