14-51333207-A-G

Variant names:

• chr14-51333207-A-G
• rs2884058
• ENST00000556479.6:n.140A>G

Variant summary

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

The ENST00000556479.6(LINC00640):​n.140A>G 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 0.927 in 152,284 control chromosomes in the GnomAD database, including 65,531 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 0.93 (65531 hom., cov: 32)
• Consequence: LINC00640 ENST00000556479.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103

Genes affected

LINC00640 (HGNC:44291): (long intergenic non-protein coding RNA 640)

LOC124900595 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00640	NR_038358.1	n.-186A>G		upstream_gene_variant
LOC124900595	XR_943854.3	n.*192T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00640	ENST00000556479.6	n.140A>G		non_coding_transcript_exon_variant	Exon 1 of 5	2

Frequencies

GnomAD3 genomes AF: 0.927 AC: 141100 AN: 152166 Hom.: 65472 Cov.: 32

Gnomad AFR AF: 0.958

Gnomad AMI AF: 0.889

Gnomad AMR AF: 0.922

Gnomad ASJ AF: 0.893

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.927

Gnomad FIN AF: 0.936

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.907

Gnomad OTH AF: 0.915

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.927 AC: 141218 AN: 152284 Hom.: 65531 Cov.: 32 AF XY: 0.928 AC XY: 69070 AN XY: 74452

Gnomad4 AFR AF: 0.958

Gnomad4 AMR AF: 0.922

Gnomad4 ASJ AF: 0.893

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.927

Gnomad4 FIN AF: 0.936

Gnomad4 NFE AF: 0.907

Gnomad4 OTH AF: 0.915

Alfa AF: 0.911 Hom.: 26920

Bravo AF: 0.928

Asia WGS AF: 0.954 AC: 3317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2884058; hg19: chr14-51799925;