rs1134590

Positions:

• chr14-105721893-C-T

Variant summary

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

The ENST00000521393.1(IGHEP1):​n.552G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 768,000 control chromosomes in the GnomAD database, including 198,530 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 0.74 (42417 hom., cov: 30)
  • Exomes 𝑓: 0.70 (156113 hom.)
• Consequence: IGHEP1 ENST00000521393.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196

Genes affected

IGHEP1 (HGNC:5523): (immunoglobulin heavy constant epsilon P1 (pseudogene))

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IGHEP1	ENST00000521393.1	n.552G>A		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.741 AC: 111825 AN: 150944 Hom.: 42380 Cov.: 30

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.781

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.734

GnomAD3 exomes AF: 0.683 AC: 160797 AN: 235534 Hom.: 57834 AF XY: 0.693 AC XY: 88849 AN XY: 128288

Gnomad AFR exome AF: 0.859

Gnomad AMR exome AF: 0.410

Gnomad ASJ exome AF: 0.783

Gnomad EAS exome AF: 0.656

Gnomad SAS exome AF: 0.639

Gnomad FIN exome AF: 0.669

Gnomad NFE exome AF: 0.749

Gnomad OTH exome AF: 0.699

GnomAD4 exome AF: 0.703 AC: 433826 AN: 616940 Hom.: 156113 Cov.: 0 AF XY: 0.708 AC XY: 237790 AN XY: 336064

Gnomad4 AFR exome AF: 0.853

Gnomad4 AMR exome AF: 0.447

Gnomad4 ASJ exome AF: 0.770

Gnomad4 EAS exome AF: 0.501

Gnomad4 SAS exome AF: 0.667

Gnomad4 FIN exome AF: 0.678

Gnomad4 NFE exome AF: 0.750

Gnomad4 OTH exome AF: 0.724

GnomAD4 genome AF: 0.741 AC: 111897 AN: 151060 Hom.: 42417 Cov.: 30 AF XY: 0.728 AC XY: 53674 AN XY: 73686

Gnomad4 AFR AF: 0.850

Gnomad4 AMR AF: 0.541

Gnomad4 ASJ AF: 0.762

Gnomad4 EAS AF: 0.628

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.734

Alfa AF: 0.753 Hom.: 8051

Bravo AF: 0.733

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.3
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1134590; hg19: chr14-106188230;