4-14049108-T-C

Variant names:

• chr4-14049108-T-C
• rs4101199
• ENST00000715489.1:n.728-13156T>C

Variant summary

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

The ENST00000715489.1(LINC01182):​n.728-13156T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.915 in 152,192 control chromosomes in the GnomAD database, including 63,792 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 0.91 (63792 hom., cov: 32)
• Consequence: LINC01182 ENST00000715489.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 3 publications found

Genes affected

LINC01182 (HGNC:49564): (long intergenic non-protein coding RNA 1182)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715489.1. 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
	LINC01182	ENST00000715489.1		n.728-13156T>C		intron	N/A
	LINC01182	ENST00000715490.1		n.342+12672T>C		intron	N/A
	LINC01182	ENST00000715491.1		n.183-13156T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.915 AC: 139126 AN: 152074 Hom.: 63734 Cov.: 32

Gnomad AFR AF: 0.950

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.958

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.967

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.856

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.933

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

GnomAD4 genome AF: 0.915 AC: 139241 AN: 152192 Hom.: 63792 Cov.: 32 AF XY: 0.914 AC XY: 68041 AN XY: 74404

African (AFR) AF: 0.950 AC: 39450 AN: 41548

American (AMR) AF: 0.958 AC: 14620 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.922 AC: 3200 AN: 3472

East Asian (EAS) AF: 0.968 AC: 5006 AN: 5174

South Asian (SAS) AF: 0.916 AC: 4416 AN: 4822

European-Finnish (FIN) AF: 0.856 AC: 9082 AN: 10606

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.888 AC: 60356 AN: 67986

Other (OTH) AF: 0.934 AC: 1975 AN: 2114

Alfa AF: 0.898 Hom.: 33144

Bravo AF: 0.925

Asia WGS AF: 0.949 AC: 3295 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.32
DANN	Benign	0.51
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4101199; hg19: chr4-14050732;