rs4147732

Positions:

• chr5-53560216-T-A

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 0.204 in 152,156 control chromosomes in the GnomAD database, including 3,692 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 0.20 (3692 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30957 AN: 152038 Hom.: 3692 Cov.: 33

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.204 AC: 30982 AN: 152156 Hom.: 3692 Cov.: 33 AF XY: 0.206 AC XY: 15306 AN XY: 74398

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.211

Alfa AF: 0.171 Hom.: 379

Bravo AF: 0.213

Asia WGS AF: 0.347 AC: 1205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	7.3
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4147732; hg19: chr5-52856046;