rs4128590

Variant names:

• chr11-131354553-T-C
• rs4128590

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 0.134 in 152,190 control chromosomes in the GnomAD database, including 1,640 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 0.13 (1640 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 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: 0.134 AC: 20349 AN: 152072 Hom.: 1624 Cov.: 33

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0851

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.0464

Gnomad SAS AF: 0.0518

Gnomad FIN AF: 0.0944

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.134 AC: 20400 AN: 152190 Hom.: 1640 Cov.: 33 AF XY: 0.130 AC XY: 9680 AN XY: 74422

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.0850

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.0465

Gnomad4 SAS AF: 0.0513

Gnomad4 FIN AF: 0.0944

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.100

Alfa AF: 0.114 Hom.: 1566

Bravo AF: 0.138

Asia WGS AF: 0.0890 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.0
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4128590; hg19: chr11-131224448;