rs12590520

Variant names:

• chr14-76249591-T-C
• rs12590520
• ENST00000554225.1:n.188-2460T>C

Variant summary

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

The ENST00000554225.1(ENSG00000258454):​n.188-2460T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 152,150 control chromosomes in the GnomAD database, including 12,676 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 0.38 (12676 hom., cov: 33)
• Consequence: ENSG00000258454 ENST00000554225.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.949
• Publications: 3 publications found

Genes affected

ENSG00000258454 (HGNC:):

GPATCH2L (HGNC:20210): (G-patch domain containing 2 like)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370575	XR_001750833.3	n.663-20941A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258454	ENST00000554225.1	n.188-2460T>C		intron_variant	Intron 1 of 2	3
GPATCH2L	ENST00000556372.2	n.*118-2460T>C		intron_variant	Intron 2 of 3	3		ENSP00000451827.2
ENSG00000258402	ENST00000720628.1	n.451-20941A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57909 AN: 152032 Hom.: 12674 Cov.: 33

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.381 AC: 57927 AN: 152150 Hom.: 12676 Cov.: 33 AF XY: 0.386 AC XY: 28732 AN XY: 74392

African (AFR) AF: 0.158 AC: 6547 AN: 41528

American (AMR) AF: 0.435 AC: 6651 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1483 AN: 3470

East Asian (EAS) AF: 0.699 AC: 3626 AN: 5186

South Asian (SAS) AF: 0.468 AC: 2259 AN: 4824

European-Finnish (FIN) AF: 0.482 AC: 5092 AN: 10566

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30729 AN: 67972

Other (OTH) AF: 0.387 AC: 817 AN: 2112

Alfa AF: 0.422 Hom.: 14986

Bravo AF: 0.369

Asia WGS AF: 0.521 AC: 1808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.21
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs12590520; hg19: chr14-76715934;