11-129609280-C-T

Variant names:

• chr11-129609280-C-T
• rs1873873
• ENST00000626400.2:n.131-2432C>T

Variant summary

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

The ENST00000626400.2(ENSG00000281386):​n.131-2432C>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 ENST00000626400.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660
• Publications: 4 publications found

Genes affected

ENSG00000281386 (HGNC:):

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 (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	ENST00000626400.2	n.131-2432C>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

African (AFR) AF: 0.516 AC: 21370 AN: 41444

American (AMR) AF: 0.528 AC: 8067 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2211 AN: 3470

East Asian (EAS) AF: 0.457 AC: 2353 AN: 5148

South Asian (SAS) AF: 0.592 AC: 2853 AN: 4820

European-Finnish (FIN) AF: 0.440 AC: 4651 AN: 10582

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.522 AC: 35467 AN: 67978

Other (OTH) AF: 0.539 AC: 1136 AN: 2108

Alfa AF: 0.525 Hom.: 66594

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
PhyloP100		-0.066

Splicing

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

Other links and lift over

dbSNP: rs1873873; hg19: chr11-129479175;