rs1553477

Positions:

• chr5-53821136-A-C

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 0.502 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.546

Gnomad4 OTH AF: 0.495

Alfa AF: 0.522 Hom.: 8974

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1553477; hg19: chr5-53116966;