rs11134044

Variant names:

• chr5-4305048-A-G
• rs11134044

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 0.176 in 152,140 control chromosomes in the GnomAD database, including 2,407 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 0.18 (2407 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.687

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.219 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: 0.176 AC: 26801 AN: 152022 Hom.: 2408 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.176 AC: 26814 AN: 152140 Hom.: 2407 Cov.: 32 AF XY: 0.173 AC XY: 12867 AN XY: 74374

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.212

Alfa AF: 0.166 Hom.: 2092

Bravo AF: 0.185

Asia WGS AF: 0.132 AC: 460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.86
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11134044; hg19: chr5-4305161;