rs4754450

Variant names:

• chr11-110426324-T-C
• rs4754450

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 0.519 in 152,012 control chromosomes in the GnomAD database, including 21,930 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 0.52 (21930 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.711 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: 0.518 AC: 78714 AN: 151894 Hom.: 21878 Cov.: 32

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.519 AC: 78829 AN: 152012 Hom.: 21930 Cov.: 32 AF XY: 0.520 AC XY: 38664 AN XY: 74294

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.634

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.497

Alfa AF: 0.390 Hom.: 1792

Bravo AF: 0.539

Asia WGS AF: 0.566 AC: 1968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4754450; hg19: chr11-110297048;