rs16844716

chr1-199387388-A-C

Variant summary

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

The ENST00000430498.1(EEF1A1P44):n.248A>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0246 in 192,330 control chromosomes in the GnomAD database, including 236 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 0.030 (226 hom., cov: 32)
  • Exomes 𝑓: 0.0045 (10 hom.)
• Consequence: EEF1A1P44 ENST00000430498.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.52

Genes affected

EEF1A1P44 (HGNC:56201): (eukaryotic translation elongation factor 1 alpha 1 pseudogene 44)

LINC02789 (HGNC:54310): (long intergenic non-protein coding RNA 2789)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0987 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02789	NR_147896.1	n.310-3933A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EEF1A1P44	ENST00000430498.1	n.248A>C		non_coding_transcript_exon_variant	1/1
LINC02789	ENST00000452199.1	n.310-3933A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0298 AC: 4534 AN: 152088 Hom.: 224 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0140

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.000956

Gnomad OTH AF: 0.0225

GnomAD4 exome AF: 0.00449 AC: 180 AN: 40124 Hom.: 10 Cov.: 0 AF XY: 0.00320 AC XY: 76 AN XY: 23754

Gnomad4 AFR exome AF: 0.106

Gnomad4 AMR exome AF: 0.00566

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000437

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000491

Gnomad4 OTH exome AF: 0.000639

GnomAD4 genome AF: 0.0298 AC: 4542 AN: 152206 Hom.: 226 Cov.: 32 AF XY: 0.0295 AC XY: 2192 AN XY: 74424

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.0140

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000829

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000956

Gnomad4 OTH AF: 0.0222

Alfa AF: 0.00524 Hom.: 31

Bravo AF: 0.0344

Asia WGS AF: 0.00606 AC: 21 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
Cadd	Benign	3.6
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16844716; hg19: chr1-199356516;