14-90489716-C-T

Variant names:

• chr14-90489716-C-T
• rs1294497
• ENST00000567837.1:n.1922G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000647570.1(ENSG00000259789):​n.391G>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 0.574 in 152,150 control chromosomes in the GnomAD database, including 26,000 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 0.57 (25996 hom., cov: 33)
  • Exomes 𝑓: 0.50 (4 hom.)
• Consequence: ENSG00000259789 ENST00000647570.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526
• Publications: 5 publications found

Genes affected

ENSG00000259789 (HGNC:):

LINC00642 (HGNC:44293): (long intergenic non-protein coding RNA 642)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647570.1. 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
	ENSG00000259789	ENST00000567837.1	TSL:6	n.1922G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000259789	ENST00000647570.1		n.391G>A		non_coding_transcript_exon	Exon 4 of 4
	LINC00642	ENST00000655041.1		n.304-17C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87243 AN: 152002 Hom.: 25945 Cov.: 33

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.593

GnomAD4 exome AF: 0.500 AC: 15 AN: 30 Hom.: 4 Cov.: 0 AF XY: 0.455 AC XY: 10 AN XY: 22

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 11 AN: 22

Other (OTH) AF: 0.500 AC: 4 AN: 8

GnomAD4 genome AF: 0.574 AC: 87359 AN: 152120 Hom.: 25996 Cov.: 33 AF XY: 0.581 AC XY: 43172 AN XY: 74360

African (AFR) AF: 0.703 AC: 29176 AN: 41520

American (AMR) AF: 0.663 AC: 10137 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1969 AN: 3470

East Asian (EAS) AF: 0.725 AC: 3742 AN: 5162

South Asian (SAS) AF: 0.608 AC: 2931 AN: 4818

European-Finnish (FIN) AF: 0.495 AC: 5241 AN: 10586

Middle Eastern (MID) AF: 0.558 AC: 163 AN: 292

European-Non Finnish (NFE) AF: 0.478 AC: 32490 AN: 67966

Other (OTH) AF: 0.593 AC: 1249 AN: 2108

Alfa AF: 0.511 Hom.: 57319

Bravo AF: 0.591

Asia WGS AF: 0.649 AC: 2258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.4
DANN	Benign	0.72
PhyloP100		-0.53

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: rs1294497;

hg19: chr14-90956060;