rs1817114

Positions:

• chr21-27367234-G-A

Variant summary

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

The ENST00000420241.1(EIF4A1P1):​n.714C>T 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 0.519 in 531,466 control chromosomes in the GnomAD database, including 76,376 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 0.47 (18553 hom., cov: 31)
  • Exomes 𝑓: 0.54 (57823 hom.)
• Consequence: EIF4A1P1 ENST00000420241.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428

Genes affected

EIF4A1P1 (HGNC:3283): (eukaryotic translation initiation factor 4A1 pseudogene 1)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.603 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
EIF4A1P1	ENST00000420241.1	n.714C>T		non_coding_transcript_exon_variant	1/1
	ENST00000420186.2	n.332-6078C>T		intron_variant, non_coding_transcript_variant		1
	ENST00000666822.1	n.399+4421G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71027 AN: 151810 Hom.: 18534 Cov.: 31

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.467

GnomAD4 exome AF: 0.539 AC: 204747 AN: 379538 Hom.: 57823 Cov.: 0 AF XY: 0.549 AC XY: 118795 AN XY: 216544

Gnomad4 AFR exome AF: 0.241

Gnomad4 AMR exome AF: 0.442

Gnomad4 ASJ exome AF: 0.493

Gnomad4 EAS exome AF: 0.193

Gnomad4 SAS exome AF: 0.573

Gnomad4 FIN exome AF: 0.506

Gnomad4 NFE exome AF: 0.597

Gnomad4 OTH exome AF: 0.519

GnomAD4 genome AF: 0.468 AC: 71063 AN: 151928 Hom.: 18553 Cov.: 31 AF XY: 0.462 AC XY: 34303 AN XY: 74226

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.471

Alfa AF: 0.520 Hom.: 4185

Bravo AF: 0.448

Asia WGS AF: 0.353 AC: 1228 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	3.2
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1817114; hg19: chr21-28739553;