4-4847743-T-C

Variant names:

• chr4-4847743-T-C
• rs11726039
• ENST00000609099.1:n.406+234T>C

Variant summary

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

The ENST00000609099.1(LINC01396):​n.406+234T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 150,354 control chromosomes in the GnomAD database, including 10,361 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 0.36 (10361 hom., cov: 30)
• Consequence: LINC01396 ENST00000609099.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285
• Publications: 2 publications found

Genes affected

LINC01396 (HGNC:50675): (long intergenic non-protein coding RNA 1396)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01396	NR_125765.1	n.406+234T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01396	ENST00000609099.1	n.406+234T>C		intron_variant	Intron 3 of 3	3
LINC01396	ENST00000652410.1	n.1226+312T>C		intron_variant	Intron 3 of 3
LINC01396	ENST00000662851.1	n.1136+2420T>C		intron_variant	Intron 1 of 1
LINC01396	ENST00000724736.1	n.368-2964T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54444 AN: 150244 Hom.: 10339 Cov.: 30

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.0855

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.363 AC: 54507 AN: 150354 Hom.: 10361 Cov.: 30 AF XY: 0.360 AC XY: 26383 AN XY: 73274

African (AFR) AF: 0.465 AC: 19010 AN: 40858

American (AMR) AF: 0.395 AC: 5952 AN: 15070

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1472 AN: 3460

East Asian (EAS) AF: 0.0851 AC: 431 AN: 5064

South Asian (SAS) AF: 0.226 AC: 1059 AN: 4680

European-Finnish (FIN) AF: 0.336 AC: 3433 AN: 10226

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.323 AC: 21891 AN: 67724

Other (OTH) AF: 0.368 AC: 763 AN: 2072

Alfa AF: 0.239 Hom.: 732

Bravo AF: 0.372

Asia WGS AF: 0.197 AC: 686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
DANN	Benign	0.84
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs11726039; hg19: chr4-4849470;