rs11134612

Variant names:

• chr5-170124232-G-A
• rs11134612

Your query was ambiguous. Multiple possible variants found:

• chr5-170124232-G-A
• chr5-170124232-G-T

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 0.167 in 152,154 control chromosomes in the GnomAD database, including 2,255 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 0.17 (2255 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.18 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: 0.167 AC: 25356 AN: 152036 Hom.: 2249 Cov.: 33

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0565

Gnomad SAS AF: 0.0968

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.167 AC: 25384 AN: 152154 Hom.: 2255 Cov.: 33 AF XY: 0.167 AC XY: 12421 AN XY: 74398

African (AFR) AF: 0.154 AC: 6393 AN: 41488

American (AMR) AF: 0.130 AC: 1988 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 444 AN: 3470

East Asian (EAS) AF: 0.0559 AC: 289 AN: 5174

South Asian (SAS) AF: 0.0975 AC: 470 AN: 4820

European-Finnish (FIN) AF: 0.265 AC: 2810 AN: 10584

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12420 AN: 68008

Other (OTH) AF: 0.154 AC: 325 AN: 2112

Alfa AF: 0.163 Hom.: 1260

Bravo AF: 0.158

Asia WGS AF: 0.0950 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.70
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs11134612; hg19: chr5-169551236;