rs505703

Positions:

• chr4-13919358-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_121681.1(LINC01182):​n.350-9992C>T variant causes a intron, non coding transcript 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 NR_121681.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

Genes affected

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

LOC107986182 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC01182	NR_121681.1	n.350-9992C>T		intron_variant, non_coding_transcript_variant
LOC107986182	XR_001741382.2	n.3015-12186C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01182	ENST00000669061.1	n.713+80899C>T		intron_variant, non_coding_transcript_variant
LINC01182	ENST00000503532.1	n.231-40631C>T		intron_variant, non_coding_transcript_variant		4
LINC01182	ENST00000510907.5	n.350-9992C>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.208

Alfa AF: 0.173 Hom.: 3264

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs505703; hg19: chr4-13920982;