rs16844716

Variant names:

• chr1-199387388-A-C
• rs16844716
• ENST00000430498.1:n.248A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000430498.1. 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
	LINC02789	NR_147896.1		n.310-3933A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EEF1A1P44	ENST00000430498.1	TSL:6	n.248A>C		non_coding_transcript_exon	Exon 1 of 1
	LINC02789	ENST00000452199.1	TSL:2	n.310-3933A>C		intron	N/A

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

African (AFR) AF: 0.106 AC: 135 AN: 1270

American (AMR) AF: 0.00566 AC: 32 AN: 5654

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 546

East Asian (EAS) AF: 0.00 AC: 0 AN: 2500

South Asian (SAS) AF: 0.000437 AC: 2 AN: 4578

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3614

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 46

European-Non Finnish (NFE) AF: 0.000491 AC: 10 AN: 20352

Other (OTH) AF: 0.000639 AC: 1 AN: 1564

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

African (AFR) AF: 0.101 AC: 4205 AN: 41524

American (AMR) AF: 0.0140 AC: 214 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5168

South Asian (SAS) AF: 0.000829 AC: 4 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10632

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.000956 AC: 65 AN: 67988

Other (OTH) AF: 0.0222 AC: 47 AN: 2114

Alfa AF: 0.0151 Hom.: 177

Bravo AF: 0.0344

Asia WGS AF: 0.00606 AC: 21 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	3.6
DANN	Benign	0.81
PhyloP100		6.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16844716;

hg19: chr1-199356516;