XR_007058947.1:n.-8C>T

Variant names:

• chr5-135890448-C-T
• rs11741137
• XR_007058947.1:n.-8C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007058947.1(LOC124901074):​n.-8C>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
• Publications: 15 publications found

Genes affected

LOC124901074 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.127 AC: 5282 AN: 41484

American (AMR) AF: 0.0831 AC: 1271 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 547 AN: 3468

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5182

South Asian (SAS) AF: 0.104 AC: 500 AN: 4816

European-Finnish (FIN) AF: 0.150 AC: 1585 AN: 10592

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

European-Non Finnish (NFE) AF: 0.134 AC: 9091 AN: 68004

Other (OTH) AF: 0.106 AC: 224 AN: 2110

Alfa AF: 0.126 Hom.: 2068

Bravo AF: 0.117

Asia WGS AF: 0.0760 AC: 265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.2
DANN	Benign	0.64
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs11741137; hg19: chr5-135226137;