rs9268589

Variant names:

• chr6-32430425-G-A
• rs9268589
• ENST00000766007.1:n.586C>T

Variant summary

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

The ENST00000766007.1(ENSG00000299747):​n.586C>T 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 0.387 in 151,970 control chromosomes in the GnomAD database, including 11,698 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 0.39 (11698 hom., cov: 31)
• Consequence: ENSG00000299747 ENST00000766007.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.825
• Publications: 24 publications found

Genes affected

ENSG00000299747 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766007.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299747	ENST00000766007.1		n.586C>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000299769	ENST00000766247.1		n.283-3667G>A		intron	N/A
	ENSG00000299769	ENST00000766248.1		n.392-289G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58746 AN: 151852 Hom.: 11697 Cov.: 31

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.387 AC: 58767 AN: 151970 Hom.: 11698 Cov.: 31 AF XY: 0.389 AC XY: 28897 AN XY: 74288

African (AFR) AF: 0.341 AC: 14136 AN: 41426

American (AMR) AF: 0.448 AC: 6838 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1797 AN: 3470

East Asian (EAS) AF: 0.553 AC: 2854 AN: 5162

South Asian (SAS) AF: 0.521 AC: 2503 AN: 4808

European-Finnish (FIN) AF: 0.291 AC: 3078 AN: 10562

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26192 AN: 67952

Other (OTH) AF: 0.412 AC: 869 AN: 2110

Alfa AF: 0.397 Hom.: 43972

Bravo AF: 0.395

Asia WGS AF: 0.472 AC: 1641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.0
DANN	Benign	0.60
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs9268589; hg19: chr6-32398202;