rs1552222

Variant names:

• chr19-41019999-T-A
• rs1552222

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 0.177 in 152,072 control chromosomes in the GnomAD database, including 2,535 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 0.18 (2535 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.258 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: 0.177 AC: 26881 AN: 151956 Hom.: 2532 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0863

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.177 AC: 26911 AN: 152072 Hom.: 2535 Cov.: 32 AF XY: 0.177 AC XY: 13152 AN XY: 74304

African (AFR) AF: 0.229 AC: 9513 AN: 41464

American (AMR) AF: 0.122 AC: 1861 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0863 AC: 299 AN: 3466

East Asian (EAS) AF: 0.270 AC: 1399 AN: 5178

South Asian (SAS) AF: 0.168 AC: 808 AN: 4814

European-Finnish (FIN) AF: 0.171 AC: 1809 AN: 10558

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10692 AN: 67990

Other (OTH) AF: 0.164 AC: 346 AN: 2114

Alfa AF: 0.164 Hom.: 276

Bravo AF: 0.176

Asia WGS AF: 0.197 AC: 687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.3
DANN	Benign	0.14
PhyloP100		-0.022

Splicing

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

Other links and lift over

dbSNP: rs1552222; hg19: chr19-41525904;