ENST00000753986.1:n.116+4379T>G

Variant names:

• chr1-234590266-A-C
• rs744487
• ENST00000753986.1:n.116+4379T>G

Variant summary

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

The ENST00000753986.1(ENSG00000286210):​n.116+4379T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 152,074 control chromosomes in the GnomAD database, including 6,693 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 0.29 (6693 hom., cov: 32)
• Consequence: ENSG00000286210 ENST00000753986.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12
• Publications: 15 publications found

Genes affected

ENSG00000286210 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.318 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
ENSG00000286210	ENST00000753986.1	n.116+4379T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44572 AN: 151956 Hom.: 6690 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.293 AC: 44598 AN: 152074 Hom.: 6693 Cov.: 32 AF XY: 0.289 AC XY: 21466 AN XY: 74316

African (AFR) AF: 0.276 AC: 11456 AN: 41484

American (AMR) AF: 0.248 AC: 3798 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1254 AN: 3470

East Asian (EAS) AF: 0.218 AC: 1125 AN: 5166

South Asian (SAS) AF: 0.184 AC: 888 AN: 4822

European-Finnish (FIN) AF: 0.307 AC: 3245 AN: 10576

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21850 AN: 67956

Other (OTH) AF: 0.300 AC: 633 AN: 2110

Alfa AF: 0.307 Hom.: 23323

Bravo AF: 0.290

Asia WGS AF: 0.209 AC: 730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.1
DANN	Benign	0.77
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs744487; hg19: chr1-234726012;