rs1553477

Variant names:

• chr5-53821136-A-C
• rs1553477

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 0.502 in 152,150 control chromosomes in the GnomAD database, including 19,679 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 0.50 (19679 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.541 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: 0.502 AC: 76320 AN: 152032 Hom.: 19669 Cov.: 33

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.502 AC: 76373 AN: 152150 Hom.: 19679 Cov.: 33 AF XY: 0.495 AC XY: 36838 AN XY: 74378

African (AFR) AF: 0.474 AC: 19667 AN: 41516

American (AMR) AF: 0.484 AC: 7398 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1960 AN: 3472

East Asian (EAS) AF: 0.234 AC: 1211 AN: 5174

South Asian (SAS) AF: 0.314 AC: 1515 AN: 4826

European-Finnish (FIN) AF: 0.541 AC: 5726 AN: 10580

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.546 AC: 37099 AN: 67978

Other (OTH) AF: 0.495 AC: 1047 AN: 2114

Alfa AF: 0.522 Hom.: 10703

Bravo AF: 0.500

Asia WGS AF: 0.297 AC: 1030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.51
DANN	Benign	0.53
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1553477; hg19: chr5-53116966;