chr7-143477799-A-G

Position:

• chr7-143477799-A-G

Variant summary

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

The ENST00000429289.5(EPHA1-AS1):​n.207-26975A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 1,443,876 control chromosomes in the GnomAD database, including 420,977 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 0.78 (46242 hom., cov: 29)
  • Exomes 𝑓: 0.76 (374735 hom.)
• Consequence: EPHA1-AS1 ENST00000429289.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510

Genes affected

EPHA1-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EPHA1-AS1	NR_033897.1	n.207-26975A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EPHA1-AS1	ENST00000429289.5	n.207-26975A>G		intron_variant		1
EPHA1-AS1	ENST00000690912.1	n.228-18167A>G		intron_variant
EPHA1-AS1	ENST00000703017.1	n.206-18167A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.777 AC: 117998 AN: 151844 Hom.: 46198 Cov.: 29

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.788

GnomAD4 exome AF: 0.761 AC: 982632 AN: 1291914 Hom.: 374735 AF XY: 0.759 AC XY: 490864 AN XY: 646898

Gnomad4 AFR exome AF: 0.854

Gnomad4 AMR exome AF: 0.735

Gnomad4 ASJ exome AF: 0.761

Gnomad4 EAS exome AF: 0.620

Gnomad4 SAS exome AF: 0.709

Gnomad4 FIN exome AF: 0.764

Gnomad4 NFE exome AF: 0.769

Gnomad4 OTH exome AF: 0.757

GnomAD4 genome AF: 0.777 AC: 118102 AN: 151962 Hom.: 46242 Cov.: 29 AF XY: 0.774 AC XY: 57495 AN XY: 74258

Gnomad4 AFR AF: 0.847

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.756

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.772

Gnomad4 NFE AF: 0.764

Gnomad4 OTH AF: 0.790

Alfa AF: 0.761 Hom.: 20322

Bravo AF: 0.780

Asia WGS AF: 0.692 AC: 2408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1404634; hg19: chr7-143174892; COSMIC: COSV68765264;