rs4128590

chr11-131354553-T-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 0.134 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;