rs11741137

chr5-135890448-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The 5-135890448-C-T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,160 control chromosomes in the GnomAD database, including 1,222 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 0.12 (1222 hom., cov: 32)
• Consequence: LOC124901074 XR_007058947.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.693

Genes affected

LOC124901074 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901074	XR_007058947.1			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18761 AN: 152042 Hom.: 1220 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.0833

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.123 AC: 18771 AN: 152160 Hom.: 1222 Cov.: 32 AF XY: 0.123 AC XY: 9143 AN XY: 74386

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.0831

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.106

Alfa AF: 0.127 Hom.: 1633

Bravo AF: 0.117

Asia WGS AF: 0.0760 AC: 265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	7.2
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11741137; hg19: chr5-135226137;