rs11134044

Variant names:

• chr5-4305048-A-G
• rs11134044

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.223 AC: 9253 AN: 41510

American (AMR) AF: 0.184 AC: 2816 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 679 AN: 3468

East Asian (EAS) AF: 0.115 AC: 594 AN: 5170

South Asian (SAS) AF: 0.165 AC: 794 AN: 4814

European-Finnish (FIN) AF: 0.119 AC: 1260 AN: 10590

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10677 AN: 67990

Other (OTH) AF: 0.212 AC: 448 AN: 2112

Alfa AF: 0.169 Hom.: 2806

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
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs11134044; hg19: chr5-4305161;