ENST00000442774.1:n.-30T>G

Variant names:

• chr1-30226493-T-G
• rs6684063
• ENST00000442774.1:n.-30T>G

Variant summary

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

The ENST00000442774.1(ENSG00000231251):​n.-30T>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 513,628 control chromosomes in the GnomAD database, including 30,538 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 0.35 (12943 hom., cov: 31)
  • Exomes 𝑓: 0.26 (17595 hom.)
• Consequence: ENSG00000231251 ENST00000442774.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.745
• Publications: 7 publications found

Genes affected

ENSG00000231251 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 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
ENSG00000231251	ENST00000442774.1	n.-30T>G		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53056 AN: 151702 Hom.: 12914 Cov.: 31

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.319

GnomAD4 exome AF: 0.264 AC: 95498 AN: 361806 Hom.: 17595 Cov.: 0 AF XY: 0.262 AC XY: 53251 AN XY: 203620

African (AFR) AF: 0.638 AC: 6216 AN: 9740

American (AMR) AF: 0.529 AC: 14483 AN: 27398

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 2276 AN: 11342

East Asian (EAS) AF: 0.747 AC: 10719 AN: 14348

South Asian (SAS) AF: 0.322 AC: 18861 AN: 58618

European-Finnish (FIN) AF: 0.200 AC: 6032 AN: 30192

Middle Eastern (MID) AF: 0.235 AC: 300 AN: 1274

European-Non Finnish (NFE) AF: 0.168 AC: 32277 AN: 191632

Other (OTH) AF: 0.251 AC: 4334 AN: 17262

GnomAD4 genome AF: 0.350 AC: 53144 AN: 151822 Hom.: 12943 Cov.: 31 AF XY: 0.355 AC XY: 26321 AN XY: 74192

African (AFR) AF: 0.633 AC: 26172 AN: 41366

American (AMR) AF: 0.420 AC: 6403 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 673 AN: 3468

East Asian (EAS) AF: 0.739 AC: 3788 AN: 5128

South Asian (SAS) AF: 0.336 AC: 1611 AN: 4800

European-Finnish (FIN) AF: 0.207 AC: 2182 AN: 10548

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11315 AN: 67964

Other (OTH) AF: 0.317 AC: 668 AN: 2106

Alfa AF: 0.263 Hom.: 12281

Bravo AF: 0.382

Asia WGS AF: 0.511 AC: 1776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.67
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs6684063; hg19: chr1-30699340;