ENST00000654217.1:n.153+7081G>A

Variant names:

• chr1-58553401-G-A
• rs565954
• ENST00000654217.1:n.153+7081G>A

Variant summary

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

The ENST00000654217.1(ENSG00000286918):​n.153+7081G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,058 control chromosomes in the GnomAD database, including 3,677 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 0.17 (3676 hom., cov: 32)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: ENSG00000286918 ENST00000654217.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.65

Genes affected

ENSG00000286918 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 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
ENSG00000286918	ENST00000654217.1	n.153+7081G>A		intron_variant	Intron 1 of 1
ENSG00000270209	ENST00000604022.1	n.-68C>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26509 AN: 151934 Hom.: 3656 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.0547

Gnomad FIN AF: 0.0791

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.164

GnomAD4 exome AF: 0.500 AC: 3 AN: 6 Hom.: 1 AF XY: 0.750 AC XY: 3 AN XY: 4

Gnomad4 AFR exome AF: 1.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.175 AC: 26566 AN: 152052 Hom.: 3676 Cov.: 32 AF XY: 0.169 AC XY: 12548 AN XY: 74346

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.0560

Gnomad4 FIN AF: 0.0791

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.162

Alfa AF: 0.144 Hom.: 304

Bravo AF: 0.187

Asia WGS AF: 0.0640 AC: 222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.025
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs565954; hg19: chr1-59019073;