XR_935327.3:n.70-8297A>C

Variant names:

• chr18-29245022-T-G
• rs10502519
• XR_935327.3:n.70-8297A>C

Variant summary

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

The XR_935327.3(LOC105372044):​n.70-8297A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0616 in 152,260 control chromosomes in the GnomAD database, including 314 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 0.062 (314 hom., cov: 32)
• Consequence: LOC105372044 XR_935327.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840
• Publications: 1 publications found

Genes affected

LOC105372044 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0917 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0615 AC: 9356 AN: 152142 Hom.: 314 Cov.: 32

Gnomad AFR AF: 0.0312

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0954

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.0776

Gnomad SAS AF: 0.0653

Gnomad FIN AF: 0.0532

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0738

Gnomad OTH AF: 0.0593

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

GnomAD4 genome AF: 0.0616 AC: 9377 AN: 152260 Hom.: 314 Cov.: 32 AF XY: 0.0606 AC XY: 4510 AN XY: 74450

African (AFR) AF: 0.0313 AC: 1303 AN: 41564

American (AMR) AF: 0.0958 AC: 1464 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0389 AC: 135 AN: 3470

East Asian (EAS) AF: 0.0780 AC: 404 AN: 5180

South Asian (SAS) AF: 0.0651 AC: 314 AN: 4822

European-Finnish (FIN) AF: 0.0532 AC: 565 AN: 10616

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0738 AC: 5022 AN: 68004

Other (OTH) AF: 0.0587 AC: 124 AN: 2112

Alfa AF: 0.0633 Hom.: 40

Bravo AF: 0.0632

Asia WGS AF: 0.0570 AC: 199 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.68
PhyloP100		0.084

Splicing

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

Other links and lift over

dbSNP: rs10502519; hg19: chr18-26824987;