rs11260603

Variant names:

• chr1-1143818-T-C
• rs11260603
• ENST00000416774.1:n.1382T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-1143818-T-C
• chr1-1143818-T-G

Variant summary

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

The ENST00000416774.1(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 ENST00000416774.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.69
• Publications: 7 publications found

Genes affected

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

LOC124903820 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416774.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01342	NR_038869.1		n.1382T>C		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01342	ENST00000416774.1	TSL:1	n.1382T>C		non_coding_transcript_exon	Exon 3 of 3

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

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 1 AN: 4

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AF: 0.400 AC: 4 AN: 10

European-Finnish (FIN) AF: 0.375 AC: 3 AN: 8

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.215 AC: 40 AN: 186

Other (OTH) AF: 0.350 AC: 7 AN: 20

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

African (AFR) AF: 0.565 AC: 23348 AN: 41296

American (AMR) AF: 0.185 AC: 2823 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 675 AN: 3462

East Asian (EAS) AF: 0.0462 AC: 239 AN: 5174

South Asian (SAS) AF: 0.281 AC: 1356 AN: 4826

European-Finnish (FIN) AF: 0.333 AC: 3514 AN: 10540

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17601 AN: 67882

Other (OTH) AF: 0.267 AC: 560 AN: 2098

Alfa AF: 0.282 Hom.: 12857

Bravo AF: 0.329

Asia WGS AF: 0.167 AC: 578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.30
PhyloP100		-2.7
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11260603;

hg19: chr1-1079198;