ENST00000688327.3:n.1731C>T

Variant names:

• chr6-32892975-G-A
• rs9469300
• ENST00000688327.3:n.1731C>T

Variant summary

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

The ENST00000688327.3(ENSG00000289559):​n.1731C>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 0.129 in 152,072 control chromosomes in the GnomAD database, including 1,457 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 0.13 (1457 hom., cov: 32)
• Consequence: ENSG00000289559 ENST00000688327.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457
• Publications: 24 publications found

Genes affected

ENSG00000289559 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000688327.3. 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
	ENSG00000289559	ENST00000688327.3		n.1731C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000289559	ENST00000753352.1		n.856+612C>T		intron	N/A
	ENSG00000289559	ENST00000753353.1		n.507+612C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19598 AN: 151956 Hom.: 1451 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0954

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0868

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.129 AC: 19642 AN: 152072 Hom.: 1457 Cov.: 32 AF XY: 0.130 AC XY: 9639 AN XY: 74328

African (AFR) AF: 0.193 AC: 8016 AN: 41430

American (AMR) AF: 0.0953 AC: 1456 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 641 AN: 3468

East Asian (EAS) AF: 0.0868 AC: 450 AN: 5186

South Asian (SAS) AF: 0.141 AC: 678 AN: 4822

European-Finnish (FIN) AF: 0.114 AC: 1203 AN: 10570

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6841 AN: 68002

Other (OTH) AF: 0.120 AC: 254 AN: 2110

Alfa AF: 0.110 Hom.: 4080

Bravo AF: 0.128

Asia WGS AF: 0.141 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.35
DANN	Benign	0.77
PhyloP100		-0.46

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9469300;

hg19: chr6-32860752;