ENST00000691600.2:n.1200C>T

Variant names:

• chr6-43937043-C-T
• rs11755845
• ENST00000691600.2:n.1200C>T

Variant summary

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

The ENST00000691600.2(LINC01512):​n.1200C>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 ENST00000691600.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16
• Publications: 25 publications found

Genes affected

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

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

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 = 0.267 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000691600.2. 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
	LINC01512	NR_024478.1		n.1118C>T		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01512	ENST00000691600.2		n.1200C>T		non_coding_transcript_exon	Exon 2 of 2
	LINC01512	ENST00000719667.1		n.920C>T		non_coding_transcript_exon	Exon 3 of 3
	LINC01512	ENST00000719668.1		n.859C>T		non_coding_transcript_exon	Exon 3 of 3

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

African (AFR) AF: 0.138 AC: 5741 AN: 41492

American (AMR) AF: 0.274 AC: 4190 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1190 AN: 3468

East Asian (EAS) AF: 0.164 AC: 844 AN: 5156

South Asian (SAS) AF: 0.194 AC: 934 AN: 4812

European-Finnish (FIN) AF: 0.190 AC: 2005 AN: 10544

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16795 AN: 67946

Other (OTH) AF: 0.262 AC: 553 AN: 2108

Alfa AF: 0.244 Hom.: 19999

Bravo AF: 0.220

Asia WGS AF: 0.186 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.2
DANN	Benign	0.46
PhyloP100		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: rs11755845;

hg19: chr6-43904780;