rs11134338

Variant names:

• chr5-8983609-G-A
• rs11134338

Your query was ambiguous. Multiple possible variants found:

• chr5-8983609-G-A
• chr5-8983609-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 0.22 in 151,958 control chromosomes in the GnomAD database, including 3,903 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 0.22 (3903 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.983
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 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: 0.220 AC: 33421 AN: 151840 Hom.: 3902 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.220 AC: 33458 AN: 151958 Hom.: 3903 Cov.: 32 AF XY: 0.214 AC XY: 15881 AN XY: 74254

African (AFR) AF: 0.275 AC: 11398 AN: 41408

American (AMR) AF: 0.180 AC: 2746 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 709 AN: 3470

East Asian (EAS) AF: 0.104 AC: 535 AN: 5146

South Asian (SAS) AF: 0.174 AC: 836 AN: 4802

European-Finnish (FIN) AF: 0.126 AC: 1333 AN: 10578

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15088 AN: 67976

Other (OTH) AF: 0.227 AC: 479 AN: 2110

Alfa AF: 0.224 Hom.: 13132

Bravo AF: 0.227

Asia WGS AF: 0.191 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.41
DANN	Benign	0.42
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs11134338; hg19: chr5-8983721;