rs11134338

chr5-8983609-G-Achr5-8983609-G-T

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 0.22 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.227

Alfa AF: 0.224 Hom.: 7837

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11134338; hg19: chr5-8983721;