rs2111505

Variant names:

• chr19-32288713-C-A
• rs2111505

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 0.226 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
• Publications: 4 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.112 AC: 4660 AN: 41516

American (AMR) AF: 0.376 AC: 5740 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 906 AN: 3466

East Asian (EAS) AF: 0.313 AC: 1614 AN: 5162

South Asian (SAS) AF: 0.215 AC: 1038 AN: 4824

European-Finnish (FIN) AF: 0.297 AC: 3149 AN: 10594

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16557 AN: 67996

Other (OTH) AF: 0.232 AC: 490 AN: 2108

Alfa AF: 0.241 Hom.: 20261

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
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs2111505; hg19: chr19-32779619;