rs1817114

Variant names:

• chr21-27367234-G-A
• rs1817114
• ENST00000420186.2:n.332-6078C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000231236 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420241.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000231236	ENST00000420186.2	TSL:1	n.332-6078C>T		intron	N/A
	ENSG00000236332	ENST00000447384.1	TSL:1	n.391+4421G>A		intron	N/A
	EIF4A1P1	ENST00000420241.1	TSL:6	n.714C>T		non_coding_transcript_exon	Exon 1 of 1

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

African (AFR) AF: 0.241 AC: 2667 AN: 11066

American (AMR) AF: 0.442 AC: 15843 AN: 35878

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 5972 AN: 12120

East Asian (EAS) AF: 0.193 AC: 3035 AN: 15750

South Asian (SAS) AF: 0.573 AC: 37651 AN: 65690

European-Finnish (FIN) AF: 0.506 AC: 9162 AN: 18124

Middle Eastern (MID) AF: 0.471 AC: 616 AN: 1308

European-Non Finnish (NFE) AF: 0.597 AC: 120501 AN: 201678

Other (OTH) AF: 0.519 AC: 9300 AN: 17924

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

African (AFR) AF: 0.252 AC: 10463 AN: 41442

American (AMR) AF: 0.461 AC: 7034 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1740 AN: 3464

East Asian (EAS) AF: 0.190 AC: 978 AN: 5146

South Asian (SAS) AF: 0.571 AC: 2742 AN: 4802

European-Finnish (FIN) AF: 0.494 AC: 5200 AN: 10534

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41306 AN: 67954

Other (OTH) AF: 0.471 AC: 996 AN: 2116

Alfa AF: 0.513 Hom.: 4214

Bravo AF: 0.448

Asia WGS AF: 0.353 AC: 1228 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	3.2
DANN	Benign	0.52
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs1817114; hg19: chr21-28739553;