chr18-52182590-A-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372121	XR_001753538.1	n.512-31773A>G		intron_variant	Intron 4 of 6
LOC105372121	XR_001753539.1	n.341-31773A>G		intron_variant	Intron 3 of 5
LOC105372121	XR_935473.1	n.512-31773A>G		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;