chr4-13914727-G-T

Variant names:

• chr4-13914727-G-T
• rs7676721
• ENST00000503532.1:n.231-45262G>T

Variant summary

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

The ENST00000503532.1(LINC01182):​n.231-45262G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 151,990 control chromosomes in the GnomAD database, including 8,674 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 0.33 (8674 hom., cov: 32)
• Consequence: LINC01182 ENST00000503532.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• Publications: 2 publications found

Genes affected

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

ENSG00000306343 (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 = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01182	NR_121681.1	n.350-14623G>T		intron_variant	Intron 3 of 3
LOC107986182	XR_001741382.2	n.3015-16817G>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01182	ENST00000503532.1	n.231-45262G>T		intron_variant	Intron 2 of 4	4
LINC01182	ENST00000510907.5	n.350-14623G>T		intron_variant	Intron 3 of 3	2
LINC01182	ENST00000669061.1	n.713+76268G>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49701 AN: 151872 Hom.: 8653 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.327 AC: 49761 AN: 151990 Hom.: 8674 Cov.: 32 AF XY: 0.332 AC XY: 24636 AN XY: 74284

African (AFR) AF: 0.435 AC: 18040 AN: 41440

American (AMR) AF: 0.394 AC: 6011 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1210 AN: 3470

East Asian (EAS) AF: 0.256 AC: 1319 AN: 5152

South Asian (SAS) AF: 0.307 AC: 1477 AN: 4814

European-Finnish (FIN) AF: 0.318 AC: 3357 AN: 10558

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17275 AN: 67970

Other (OTH) AF: 0.352 AC: 743 AN: 2112

Alfa AF: 0.277 Hom.: 3520

Bravo AF: 0.337

Asia WGS AF: 0.317 AC: 1101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.43
PhyloP100		0.027

Splicing

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

Other links and lift over

dbSNP: rs7676721; hg19: chr4-13916351;