ENST00000789023.1:n.378+10012T>C

Variant names:

• chr4-68726064-A-G
• rs293428
• ENST00000789023.1:n.378+10012T>C

Variant summary

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

The ENST00000789023.1(ENSG00000302711):​n.378+10012T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 152,114 control chromosomes in the GnomAD database, including 10,808 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 0.36 (10808 hom., cov: 33)
• Consequence: ENSG00000302711 ENST00000789023.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 16 publications found

Genes affected

ENSG00000302711 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302711	ENST00000789023.1	n.378+10012T>C		intron_variant	Intron 2 of 4
ENSG00000302711	ENST00000789024.1	n.288+10012T>C		intron_variant	Intron 2 of 5
ENSG00000302711	ENST00000789025.1	n.245+10012T>C		intron_variant	Intron 2 of 4
ENSG00000302711	ENST00000789026.1	n.132+10012T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55132 AN: 151996 Hom.: 10771 Cov.: 33

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.363 AC: 55245 AN: 152114 Hom.: 10808 Cov.: 33 AF XY: 0.369 AC XY: 27441 AN XY: 74352

African (AFR) AF: 0.458 AC: 19019 AN: 41496

American (AMR) AF: 0.431 AC: 6587 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 718 AN: 3468

East Asian (EAS) AF: 0.598 AC: 3093 AN: 5172

South Asian (SAS) AF: 0.354 AC: 1708 AN: 4828

European-Finnish (FIN) AF: 0.379 AC: 4010 AN: 10574

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.280 AC: 19057 AN: 67966

Other (OTH) AF: 0.352 AC: 743 AN: 2112

Alfa AF: 0.305 Hom.: 20252

Bravo AF: 0.371

Asia WGS AF: 0.449 AC: 1560 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.41
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs293428; hg19: chr4-69591782;