11-129609280-C-T

Variant names:

• chr11-129609280-C-T
• rs1873873
• ENST00000626400.1:n.129-2432C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000626400.1(ENSG00000281386):​n.129-2432C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 152,034 control chromosomes in the GnomAD database, including 20,605 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 0.52 (20605 hom., cov: 32)
• Consequence: ENSG00000281386 ENST00000626400.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660

Genes affected

ENSG00000281386 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.574 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
ENSG00000281386	ENST00000626400.1	n.129-2432C>T		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78631 AN: 151914 Hom.: 20595 Cov.: 32

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.517 AC: 78675 AN: 152034 Hom.: 20605 Cov.: 32 AF XY: 0.516 AC XY: 38338 AN XY: 74302

Gnomad4 AFR AF: 0.516

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.637

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.522

Gnomad4 OTH AF: 0.539

Alfa AF: 0.527 Hom.: 44042

Bravo AF: 0.519

Asia WGS AF: 0.551 AC: 1914 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	4.2
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1873873; hg19: chr11-129479175;