rs11755845

Variant names:

• chr6-43937043-C-T
• rs11755845
• ENST00000691600.1:n.1101C>T

Variant summary

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

The NR_024478.1(LINC01512):​n.1118C>T 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 0.214 in 152,020 control chromosomes in the GnomAD database, including 3,807 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 0.21 (3807 hom., cov: 32)
• Consequence: LINC01512 NR_024478.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

Genes affected

LINC01512 (HGNC:51201): (long intergenic non-protein coding RNA 1512)

SCIRT (HGNC:55341): (stem cell inhibitory RNA transcript)

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 = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01512	NR_024478.1	n.1118C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01512	ENST00000691600.1	n.1101C>T		non_coding_transcript_exon_variant	Exon 2 of 2
SCIRT	ENST00000687158.2	n.520-4867G>A		intron_variant	Intron 3 of 3
SCIRT	ENST00000687455.1	n.234-4867G>A		intron_variant	Intron 2 of 2
SCIRT	ENST00000687843.1	n.593-4867G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32432 AN: 151906 Hom.: 3797 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.214 AC: 32460 AN: 152020 Hom.: 3807 Cov.: 32 AF XY: 0.210 AC XY: 15610 AN XY: 74284

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.262

Alfa AF: 0.251 Hom.: 10287

Bravo AF: 0.220

Asia WGS AF: 0.186 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.2
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11755845; hg19: chr6-43904780;