9-126701334-C-T

Variant names:

• chr9-126701334-C-T
• rs3906146
• ENST00000671261.2:n.3179G>A

Variant summary

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

The ENST00000671261.2(ENSG00000286428):​n.3179G>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 ENST00000671261.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526
• Publications: 7 publications found

Genes affected

ENSG00000286428 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286428	ENST00000671261.2	n.3179G>A		non_coding_transcript_exon_variant	Exon 3 of 3

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

African (AFR) AF: 0.344 AC: 14275 AN: 41452

American (AMR) AF: 0.538 AC: 8227 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1624 AN: 3472

East Asian (EAS) AF: 0.852 AC: 4378 AN: 5136

South Asian (SAS) AF: 0.601 AC: 2891 AN: 4812

European-Finnish (FIN) AF: 0.572 AC: 6036 AN: 10544

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30826 AN: 67982

Other (OTH) AF: 0.436 AC: 920 AN: 2112

Alfa AF: 0.453 Hom.: 48727

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
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs3906146; hg19: chr9-129463613;