1-1143818-T-C

Position:

• chr1-1143818-T-C

Variant summary

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

The NR_038869.1(LINC01342):​n.1382T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 151,972 control chromosomes in the GnomAD database, including 10,135 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 (10126 hom., cov: 33)
  • Exomes 𝑓: 0.24 (9 hom.)
• Consequence: LINC01342 NR_038869.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.69

Genes affected

LINC01342 (HGNC:50551): (long intergenic non-protein coding RNA 1342)

LOC124903820 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01342	NR_038869.1	n.1382T>C		non_coding_transcript_exon_variant	3/3
LOC124903820	XR_007065351.1	n.76-14664T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01342	ENST00000416774.1	n.1382T>C		non_coding_transcript_exon_variant	3/3	1

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50334 AN: 151620 Hom.: 10095 Cov.: 33

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.0465

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.270

GnomAD4 exome AF: 0.237 AC: 56 AN: 236 Hom.: 9 Cov.: 0 AF XY: 0.247 AC XY: 46 AN XY: 186

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.400

Gnomad4 FIN exome AF: 0.375

Gnomad4 NFE exome AF: 0.215

Gnomad4 OTH exome AF: 0.350

GnomAD4 genome AF: 0.332 AC: 50413 AN: 151736 Hom.: 10126 Cov.: 33 AF XY: 0.331 AC XY: 24582 AN XY: 74166

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.0462

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.267

Alfa AF: 0.271 Hom.: 1894

Bravo AF: 0.329

Asia WGS AF: 0.167 AC: 578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.30
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11260603; hg19: chr1-1079198;