rs11134551

Variant names:

• chr5-157078222-A-G
• rs11134551

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 0.201 in 151,902 control chromosomes in the GnomAD database, including 3,295 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 0.20 (3295 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.381
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 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: 0.201 AC: 30441 AN: 151786 Hom.: 3288 Cov.: 31

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.201 AC: 30483 AN: 151902 Hom.: 3295 Cov.: 31 AF XY: 0.202 AC XY: 14977 AN XY: 74234

African (AFR) AF: 0.273 AC: 11279 AN: 41372

American (AMR) AF: 0.228 AC: 3473 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 596 AN: 3470

East Asian (EAS) AF: 0.115 AC: 597 AN: 5178

South Asian (SAS) AF: 0.198 AC: 950 AN: 4806

European-Finnish (FIN) AF: 0.207 AC: 2181 AN: 10538

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10751 AN: 67960

Other (OTH) AF: 0.177 AC: 374 AN: 2112

Alfa AF: 0.174 Hom.: 4755

Bravo AF: 0.209

Asia WGS AF: 0.169 AC: 590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.0
DANN	Benign	0.76
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs11134551; hg19: chr5-156505233;