ENST00000789269.1:n.589T>C

Variant names:

• chr6-156352109-T-C
• rs9397928
• ENST00000789269.1:n.589T>C

Variant summary

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

The ENST00000789269.1(ENSG00000285797):​n.589T>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 0.318 in 151,956 control chromosomes in the GnomAD database, including 8,145 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 0.32 (8145 hom., cov: 32)
• Consequence: ENSG00000285797 ENST00000789269.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 3 publications found

Genes affected

ENSG00000285797 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378071	XR_943136.3	n.489+89T>C		intron_variant	Intron 3 of 5
LOC105378071	XR_943139.3	n.580+89T>C		intron_variant	Intron 4 of 6
LOC105378071	XR_943140.3	n.580+89T>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285797	ENST00000789269.1	n.589T>C		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000285797	ENST00000648863.1	n.302+89T>C		intron_variant	Intron 2 of 3
ENSG00000287092	ENST00000663591.1	n.224+45257A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48262 AN: 151838 Hom.: 8125 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.318 AC: 48317 AN: 151956 Hom.: 8145 Cov.: 32 AF XY: 0.326 AC XY: 24215 AN XY: 74282

African (AFR) AF: 0.352 AC: 14587 AN: 41416

American (AMR) AF: 0.411 AC: 6271 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 656 AN: 3472

East Asian (EAS) AF: 0.547 AC: 2830 AN: 5176

South Asian (SAS) AF: 0.332 AC: 1594 AN: 4808

European-Finnish (FIN) AF: 0.356 AC: 3752 AN: 10540

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.260 AC: 17685 AN: 67962

Other (OTH) AF: 0.323 AC: 683 AN: 2114

Alfa AF: 0.277 Hom.: 9073

Bravo AF: 0.326

Asia WGS AF: 0.478 AC: 1658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.099
DANN	Benign	0.80
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs9397928; hg19: chr6-156673243;