rs4128753

Variant names:

• chr5-143447227-G-A
• rs4128753

Your query was ambiguous. Multiple possible variants found:

• chr5-143447227-G-A
• chr5-143447227-G-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 0.471 in 151,876 control chromosomes in the GnomAD database, including 17,215 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 0.47 (17215 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.600

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.527 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: 0.471 AC: 71528 AN: 151758 Hom.: 17205 Cov.: 31

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.471 AC: 71579 AN: 151876 Hom.: 17215 Cov.: 31 AF XY: 0.466 AC XY: 34604 AN XY: 74214

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.499

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.481

Alfa AF: 0.496 Hom.: 2311

Bravo AF: 0.461

Asia WGS AF: 0.378 AC: 1315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.27
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4128753; hg19: chr5-142826792;