4-138415015-C-T

Variant names:

• chr4-138415015-C-T
• rs1365372
• ENST00000507145.1:n.244-9033C>T

Variant summary

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

The ENST00000507145.1(LINC00499):​n.244-9033C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.861 in 152,268 control chromosomes in the GnomAD database, including 57,019 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 0.86 (57019 hom., cov: 34)
• Consequence: LINC00499 ENST00000507145.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.593
• Publications: 4 publications found

Genes affected

LINC00499 (HGNC:43436): (long intergenic non-protein coding RNA 499)

ENSG00000297834 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507145.1. 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
	LINC00499	NR_051987.1		n.245-9033C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00499	ENST00000507145.1	TSL:4	n.244-9033C>T		intron	N/A
	LINC00499	ENST00000510736.1	TSL:5	n.486-9033C>T		intron	N/A
	LINC00499	ENST00000653577.1		n.485+65165C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.861 AC: 131017 AN: 152150 Hom.: 56970 Cov.: 34

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.882

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.944

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.884

Gnomad OTH AF: 0.871

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

GnomAD4 genome AF: 0.861 AC: 131131 AN: 152268 Hom.: 57019 Cov.: 34 AF XY: 0.854 AC XY: 63574 AN XY: 74444

African (AFR) AF: 0.900 AC: 37397 AN: 41544

American (AMR) AF: 0.770 AC: 11784 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.944 AC: 3279 AN: 3472

East Asian (EAS) AF: 0.526 AC: 2730 AN: 5188

South Asian (SAS) AF: 0.786 AC: 3790 AN: 4822

European-Finnish (FIN) AF: 0.858 AC: 9087 AN: 10592

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.884 AC: 60148 AN: 68030

Other (OTH) AF: 0.865 AC: 1829 AN: 2114

Alfa AF: 0.875 Hom.: 8165

Bravo AF: 0.855

Asia WGS AF: 0.680 AC: 2368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.17
DANN	Benign	0.47
PhyloP100		-0.59

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: rs1365372;

hg19: chr4-139336169;