18-73410989-A-G

Variant names:

• chr18-73410989-A-G
• rs8089528
• XR_007066468.1:n.1180-2267T>C

Variant summary

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

The XR_007066468.1(LOC105372190):​n.1180-2267T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 152,006 control chromosomes in the GnomAD database, including 14,153 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 0.41 (14153 hom., cov: 31)
• Consequence: LOC105372190 XR_007066468.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.766
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62357 AN: 151890 Hom.: 14138 Cov.: 31

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.411 AC: 62422 AN: 152006 Hom.: 14153 Cov.: 31 AF XY: 0.405 AC XY: 30131 AN XY: 74306

African (AFR) AF: 0.606 AC: 25118 AN: 41456

American (AMR) AF: 0.381 AC: 5816 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1110 AN: 3460

East Asian (EAS) AF: 0.360 AC: 1862 AN: 5170

South Asian (SAS) AF: 0.396 AC: 1904 AN: 4808

European-Finnish (FIN) AF: 0.226 AC: 2394 AN: 10572

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22825 AN: 67944

Other (OTH) AF: 0.381 AC: 806 AN: 2114

Alfa AF: 0.271 Hom.: 1142

Bravo AF: 0.432

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.39
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs8089528; hg19: chr18-71078224;