9-126703046-A-G

Position:

• chr9-126703046-A-G

Variant summary

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

The ENST00000671261.1(ENSG00000286428):​n.831T>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 ENST00000671261.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128

Genes affected

ENSG00000286428 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286428	ENST00000671261.1	n.831T>C		non_coding_transcript_exon_variant	2/2

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

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.691

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.231

Alfa AF: 0.211 Hom.: 8575

Bravo AF: 0.277

Asia WGS AF: 0.442 AC: 1533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs867559; hg19: chr9-129465325;