ENST00000494644.1:n.-40G>A

Variant names:

• chr6-36737010-G-A
• rs1894560
• ENST00000494644.1:n.-40G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000494644.1(ENSG00000220349):​n.-40G>A variant causes a upstream gene change. The variant allele was found at a frequency of 0.314 in 152,084 control chromosomes in the GnomAD database, including 7,700 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 0.31 (7698 hom., cov: 32)
  • Exomes 𝑓: 0.35 (2 hom.)
• Consequence: ENSG00000220349 ENST00000494644.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.86

Genes affected

ENSG00000220349 (HGNC:23626):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.358 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
ENSG00000220349	ENST00000494644.1	n.-40G>A		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47737 AN: 151904 Hom.: 7695 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.296

GnomAD4 exome AF: 0.355 AC: 22 AN: 62 Hom.: 2 Cov.: 0 AF XY: 0.500 AC XY: 16 AN XY: 32

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.250

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.405

GnomAD4 genome AF: 0.314 AC: 47773 AN: 152022 Hom.: 7698 Cov.: 32 AF XY: 0.306 AC XY: 22741 AN XY: 74320

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.293

Alfa AF: 0.345 Hom.: 11672

Bravo AF: 0.310

Asia WGS AF: 0.180 AC: 627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1894560; hg19: chr6-36704787;