rs2280450

Variant names:

• chr10-124747710-C-T
• rs2280450
• ENST00000494792.1:n.*23+12676G>A

Variant summary

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

The ENST00000494792.1(ENSG00000258539):​n.*23+12676G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 152,082 control chromosomes in the GnomAD database, including 17,922 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 0.44 (17922 hom., cov: 33)
• Consequence: ENSG00000258539 ENST00000494792.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.70
• Publications: 6 publications found

Genes affected

ENSG00000258539 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258539	ENST00000494792.1	n.*23+12676G>A		intron_variant	Intron 6 of 9	5		ENSP00000455755.1

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67638 AN: 151964 Hom.: 17904 Cov.: 33

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.445 AC: 67662 AN: 152082 Hom.: 17922 Cov.: 33 AF XY: 0.452 AC XY: 33576 AN XY: 74334

African (AFR) AF: 0.143 AC: 5938 AN: 41506

American (AMR) AF: 0.566 AC: 8650 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2278 AN: 3468

East Asian (EAS) AF: 0.394 AC: 2037 AN: 5174

South Asian (SAS) AF: 0.602 AC: 2907 AN: 4828

European-Finnish (FIN) AF: 0.587 AC: 6189 AN: 10544

Middle Eastern (MID) AF: 0.517 AC: 151 AN: 292

European-Non Finnish (NFE) AF: 0.562 AC: 38211 AN: 67956

Other (OTH) AF: 0.480 AC: 1014 AN: 2112

Alfa AF: 0.521 Hom.: 7495

Bravo AF: 0.426

Asia WGS AF: 0.489 AC: 1699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	13
DANN	Benign	0.47
PhyloP100		1.7

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2280450; hg19: chr10-126436279;