9-126701334-C-T

Position:

• chr9-126701334-C-T

Variant summary

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

The ENST00000671261.1(ENSG00000286428):​n.2543G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 152,002 control chromosomes in the GnomAD database, including 16,789 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 0.46 (16789 hom., cov: 33)
• Consequence: ENSG00000286428 ENST00000671261.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526

Genes affected

ENSG00000286428 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.126701334C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286428	ENST00000671261.1	n.2543G>A		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69648 AN: 151884 Hom.: 16780 Cov.: 33

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.459 AC: 69705 AN: 152002 Hom.: 16789 Cov.: 33 AF XY: 0.470 AC XY: 34914 AN XY: 74264

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.468

Gnomad4 EAS AF: 0.852

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.436

Alfa AF: 0.456 Hom.: 31528

Bravo AF: 0.452

Asia WGS AF: 0.682 AC: 2367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.093
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3906146; hg19: chr9-129463613;