rs4147732

Variant names:

• chr5-53560216-T-A
• rs4147732

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 0.204 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.290 AC: 12023 AN: 41504

American (AMR) AF: 0.195 AC: 2976 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 623 AN: 3472

East Asian (EAS) AF: 0.464 AC: 2390 AN: 5156

South Asian (SAS) AF: 0.276 AC: 1333 AN: 4822

European-Finnish (FIN) AF: 0.126 AC: 1340 AN: 10602

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9750 AN: 67990

Other (OTH) AF: 0.211 AC: 446 AN: 2114

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
PhyloP100		-0.010
PromoterAI		-0.020	Neutral

Splicing

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

Other links and lift over

dbSNP: rs4147732; hg19: chr5-52856046;