rs1552984

Variant names:

• chr5-84638655-T-C
• rs1552984

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 0.0836 in 152,154 control chromosomes in the GnomAD database, including 659 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 0.084 (659 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.14 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: 0.0834 AC: 12683 AN: 152036 Hom.: 653 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.0857

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0637

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.0285

Gnomad FIN AF: 0.0709

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0541

Gnomad OTH AF: 0.0865

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

GnomAD4 genome AF: 0.0836 AC: 12726 AN: 152154 Hom.: 659 Cov.: 32 AF XY: 0.0867 AC XY: 6449 AN XY: 74396

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.0637

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.0290

Gnomad4 FIN AF: 0.0709

Gnomad4 NFE AF: 0.0541

Gnomad4 OTH AF: 0.0875

Alfa AF: 0.0592 Hom.: 138

Bravo AF: 0.0914

Asia WGS AF: 0.0820 AC: 284 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1552984; hg19: chr5-83934473;