rs1557553

Variant names:

• chr22-44365104-C-T
• rs1557553

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 0.125 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
• Publications: 11 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 (AMR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0812 AC: 3374 AN: 41546

American (AMR) AF: 0.351 AC: 5368 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0671 AC: 233 AN: 3472

East Asian (EAS) AF: 0.281 AC: 1453 AN: 5168

South Asian (SAS) AF: 0.154 AC: 742 AN: 4814

European-Finnish (FIN) AF: 0.113 AC: 1202 AN: 10608

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0910 AC: 6186 AN: 68010

Other (OTH) AF: 0.148 AC: 313 AN: 2108

Alfa AF: 0.109 Hom.: 5929

Bravo AF: 0.146

Asia WGS AF: 0.191 AC: 661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.7
DANN	Benign	0.62
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs1557553; hg19: chr22-44760984;