XR_001753538.1:n.512-31773A>G

Variant names:

• chr18-52182590-A-G
• rs2879414
• XR_001753538.1:n.512-31773A>G

Variant summary

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

The XR_001753538.1(LOC105372121):​n.512-31773A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 152,178 control chromosomes in the GnomAD database, including 18,844 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 0.49 (18844 hom., cov: 33)
• Consequence: LOC105372121 XR_001753538.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 6 publications found

Genes affected

LOC105372121 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.594 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: 0.490 AC: 74497 AN: 152060 Hom.: 18821 Cov.: 33

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.490 AC: 74560 AN: 152178 Hom.: 18844 Cov.: 33 AF XY: 0.481 AC XY: 35777 AN XY: 74408

African (AFR) AF: 0.600 AC: 24910 AN: 41506

American (AMR) AF: 0.402 AC: 6156 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1435 AN: 3468

East Asian (EAS) AF: 0.230 AC: 1187 AN: 5168

South Asian (SAS) AF: 0.371 AC: 1789 AN: 4824

European-Finnish (FIN) AF: 0.419 AC: 4441 AN: 10602

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.485 AC: 33005 AN: 67996

Other (OTH) AF: 0.476 AC: 1006 AN: 2112

Alfa AF: 0.484 Hom.: 70152

Bravo AF: 0.492

Asia WGS AF: 0.305 AC: 1062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.10
DANN	Benign	0.52
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2879414; hg19: chr18-49708960;