rs752237

chr19-33240894-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 0.196 in 152,158 control chromosomes in the GnomAD database, including 3,596 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 0.20 (3596 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930

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 (AFR) allele frequency at 95% confidence interval = 0.336 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: 0.196 AC: 29872 AN: 152040 Hom.: 3594 Cov.: 34

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.196 AC: 29881 AN: 152158 Hom.: 3596 Cov.: 34 AF XY: 0.198 AC XY: 14751 AN XY: 74370

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.163

Alfa AF: 0.146 Hom.: 837

Bravo AF: 0.204

Asia WGS AF: 0.199 AC: 693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.3
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs752237; hg19: chr19-33731800;