XR_944368.3:n.150-1192T>G

Variant names:

• chr5-142099500-A-C
• rs11167764
• XR_944368.3:n.150-1192T>G

Variant summary

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

The XR_944368.3(LOC105378204):​n.150-1192T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 152,052 control chromosomes in the GnomAD database, including 48,407 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 0.80 (48407 hom., cov: 31)
• Consequence: LOC105378204 XR_944368.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.881
• Publications: 39 publications found

Genes affected

LOC105378204 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.81 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: 0.798 AC: 121204 AN: 151934 Hom.: 48364 Cov.: 31

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.798 AC: 121301 AN: 152052 Hom.: 48407 Cov.: 31 AF XY: 0.801 AC XY: 59554 AN XY: 74344

African (AFR) AF: 0.788 AC: 32647 AN: 41428

American (AMR) AF: 0.822 AC: 12563 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 2855 AN: 3470

East Asian (EAS) AF: 0.830 AC: 4289 AN: 5170

South Asian (SAS) AF: 0.783 AC: 3776 AN: 4820

European-Finnish (FIN) AF: 0.849 AC: 8990 AN: 10588

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53546 AN: 67982

Other (OTH) AF: 0.812 AC: 1714 AN: 2112

Alfa AF: 0.790 Hom.: 94419

Bravo AF: 0.798

Asia WGS AF: 0.819 AC: 2847 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.27
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs11167764; hg19: chr5-141479065;