rs6883910

Variant names:

• chr5-115960385-T-G
• rs6883910
• ENST00000723762.1:n.267-734T>G

Variant summary

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

The ENST00000723762.1(LINCADL):​n.267-734T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 152,066 control chromosomes in the GnomAD database, including 9,265 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 0.34 (9265 hom., cov: 32)
• Consequence: LINCADL ENST00000723762.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277
• Publications: 3 publications found

Genes affected

LINCADL (HGNC:53956): (lincRNA adipogenesis and lipogenesis associated) This gene encodes a long noncoding RNA involved in adipocyte differentiation and fatty acid synthesis. Expression of this gene is enriched in human adipose tissue. The long noncoding RNA product of this gene has been shown to interact with cytoplasmic and nuclear proteins, and these interactions may be important in post-transcriptional regulation of lipid metabolism genes. [provided by RefSeq, Jun 2018]

ENSG00000294441 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINCADL	ENST00000723762.1	n.267-734T>G		intron_variant	Intron 1 of 1
ENSG00000294441	ENST00000723645.1	n.-227A>C		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52184 AN: 151948 Hom.: 9259 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.343 AC: 52208 AN: 152066 Hom.: 9265 Cov.: 32 AF XY: 0.339 AC XY: 25167 AN XY: 74338

African (AFR) AF: 0.308 AC: 12760 AN: 41476

American (AMR) AF: 0.282 AC: 4304 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1262 AN: 3470

East Asian (EAS) AF: 0.243 AC: 1261 AN: 5180

South Asian (SAS) AF: 0.185 AC: 891 AN: 4810

European-Finnish (FIN) AF: 0.383 AC: 4042 AN: 10564

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26685 AN: 67964

Other (OTH) AF: 0.339 AC: 715 AN: 2110

Alfa AF: 0.359 Hom.: 1714

Bravo AF: 0.334

Asia WGS AF: 0.215 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	8.0
DANN	Benign	0.83
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs6883910; hg19: chr5-115296082; COSMIC: COSV63496699;