rs505703

Variant names:

• chr4-13919358-C-T
• rs505703
• ENST00000503532.1:n.231-40631C>T

Variant summary

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

The ENST00000503532.1(LINC01182):​n.231-40631C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,060 control chromosomes in the GnomAD database, including 3,214 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 0.20 (3214 hom., cov: 33)
• Consequence: LINC01182 ENST00000503532.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178
• Publications: 4 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01182	NR_121681.1	n.350-9992C>T		intron_variant	Intron 3 of 3
LOC107986182	XR_001741382.2	n.3015-12186C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01182	ENST00000503532.1	n.231-40631C>T		intron_variant	Intron 2 of 4	4
LINC01182	ENST00000510907.5	n.350-9992C>T		intron_variant	Intron 3 of 3	2
LINC01182	ENST00000669061.1	n.713+80899C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30300 AN: 151942 Hom.: 3210 Cov.: 33

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.199 AC: 30325 AN: 152060 Hom.: 3214 Cov.: 33 AF XY: 0.203 AC XY: 15052 AN XY: 74298

African (AFR) AF: 0.237 AC: 9851 AN: 41488

American (AMR) AF: 0.292 AC: 4465 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 848 AN: 3470

East Asian (EAS) AF: 0.143 AC: 737 AN: 5156

South Asian (SAS) AF: 0.236 AC: 1136 AN: 4812

European-Finnish (FIN) AF: 0.199 AC: 2104 AN: 10582

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10625 AN: 67962

Other (OTH) AF: 0.208 AC: 437 AN: 2106

Alfa AF: 0.177 Hom.: 4333

Bravo AF: 0.207

Asia WGS AF: 0.198 AC: 688 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.2
DANN	Benign	0.47
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs505703; hg19: chr4-13920982;