11-129609280-C-T

Position:

• chr11-129609280-C-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, non coding transcript 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: ENST00000626400.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000626400.1	n.129-2432C>T		intron_variant, non_coding_transcript_variant		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;