9-126703046-A-G

Variant names:

• chr9-126703046-A-G
• rs867559
• ENST00000671261.2:n.1467T>C

Variant summary

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

The ENST00000671261.2(ENSG00000286428):​n.1467T>C 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 0.269 in 152,102 control chromosomes in the GnomAD database, including 6,487 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 0.27 (6487 hom., cov: 33)
• Consequence: ENSG00000286428 ENST00000671261.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• Publications: 33 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000671261.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286428	ENST00000671261.2		n.1467T>C		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40846 AN: 151982 Hom.: 6470 Cov.: 33

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.269 AC: 40912 AN: 152102 Hom.: 6487 Cov.: 33 AF XY: 0.280 AC XY: 20808 AN XY: 74334

African (AFR) AF: 0.306 AC: 12679 AN: 41482

American (AMR) AF: 0.356 AC: 5443 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 382 AN: 3472

East Asian (EAS) AF: 0.691 AC: 3560 AN: 5150

South Asian (SAS) AF: 0.310 AC: 1495 AN: 4816

European-Finnish (FIN) AF: 0.356 AC: 3767 AN: 10580

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12964 AN: 67988

Other (OTH) AF: 0.231 AC: 487 AN: 2112

Alfa AF: 0.221 Hom.: 18138

Bravo AF: 0.277

Asia WGS AF: 0.442 AC: 1533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.2
DANN	Benign	0.80
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs867559; hg19: chr9-129465325;