rs2111505

Positions:

• chr19-32288713-C-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 0.226 in 152,142 control chromosomes in the GnomAD database, including 4,431 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 0.23 (4431 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.368 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: 0.226 AC: 34377 AN: 152024 Hom.: 4416 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.226 AC: 34417 AN: 152142 Hom.: 4431 Cov.: 32 AF XY: 0.228 AC XY: 16988 AN XY: 74364

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.232

Alfa AF: 0.245 Hom.: 9795

Bravo AF: 0.234

Asia WGS AF: 0.258 AC: 897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.8
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2111505; hg19: chr19-32779619;