rs1552223

Variant names:

• chr19-41020047-G-A
• rs1552223

Your query was ambiguous. Multiple possible variants found:

• chr19-41020047-G-A
• chr19-41020047-G-C
• chr19-41020047-G-T

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 0.725 in 152,162 control chromosomes in the GnomAD database, including 41,566 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 0.72 (41566 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.923 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: 0.725 AC: 110173 AN: 152044 Hom.: 41508 Cov.: 32

Gnomad AFR AF: 0.931

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.725 AC: 110289 AN: 152162 Hom.: 41566 Cov.: 32 AF XY: 0.729 AC XY: 54176 AN XY: 74366

Gnomad4 AFR AF: 0.931

Gnomad4 AMR AF: 0.799

Gnomad4 ASJ AF: 0.692

Gnomad4 EAS AF: 0.662

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.599

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.731

Alfa AF: 0.644 Hom.: 39880

Bravo AF: 0.745

Asia WGS AF: 0.727 AC: 2527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.0
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1552223; hg19: chr19-41525952;