chr18-73500517-G-A

Variant names:

• chr18-73500517-G-A
• rs7240777
• XR_007066468.1:n.1180-91795C>T

Variant summary

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

The XR_007066468.1(LOC105372190):​n.1180-91795C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 151,838 control chromosomes in the GnomAD database, including 22,228 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 0.53 (22228 hom., cov: 31)
• Consequence: LOC105372190 XR_007066468.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 11 publications found

Genes affected

LOC105372190 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.676 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: 0.533 AC: 80879 AN: 151720 Hom.: 22218 Cov.: 31

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.533 AC: 80922 AN: 151838 Hom.: 22228 Cov.: 31 AF XY: 0.537 AC XY: 39857 AN XY: 74182

African (AFR) AF: 0.405 AC: 16757 AN: 41378

American (AMR) AF: 0.650 AC: 9906 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2383 AN: 3470

East Asian (EAS) AF: 0.608 AC: 3127 AN: 5146

South Asian (SAS) AF: 0.696 AC: 3355 AN: 4822

European-Finnish (FIN) AF: 0.504 AC: 5309 AN: 10528

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38193 AN: 67942

Other (OTH) AF: 0.565 AC: 1192 AN: 2110

Alfa AF: 0.561 Hom.: 91361

Bravo AF: 0.535

Asia WGS AF: 0.606 AC: 2106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.63
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs7240777; hg19: chr18-71167752;