rs1557553

Variant names:

• chr22-44365104-C-T
• rs1557553

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 0.125 in 152,206 control chromosomes in the GnomAD database, including 1,879 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 0.12 (1879 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.344 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: 0.124 AC: 18935 AN: 152088 Hom.: 1869 Cov.: 33

Gnomad AFR AF: 0.0815

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.0671

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0910

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.125 AC: 18951 AN: 152206 Hom.: 1879 Cov.: 33 AF XY: 0.130 AC XY: 9702 AN XY: 74412

Gnomad4 AFR AF: 0.0812

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.0671

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.0910

Gnomad4 OTH AF: 0.148

Alfa AF: 0.107 Hom.: 2867

Bravo AF: 0.146

Asia WGS AF: 0.191 AC: 661 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	2.7
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1557553; hg19: chr22-44760984;