ENST00000717996.1:n.1999G>C

Variant names:

• chr11-69492927-G-C
• rs537626
• ENST00000717996.1:n.1999G>C

Variant summary

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

The ENST00000717996.1(LINC01488):​n.1999G>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 0.182 in 152,250 control chromosomes in the GnomAD database, including 2,911 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 0.18 (2911 hom., cov: 33)
  • Exomes 𝑓: 0.30 (0 hom.)
• Consequence: LINC01488 ENST00000717996.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.782
• Publications: 21 publications found

Genes affected

LINC01488 (HGNC:51144): (long intergenic non-protein coding RNA 1488)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717996.1. 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
	LINC01488	NR_185875.1	MANE Select	n.1999G>C		non_coding_transcript_exon	Exon 4 of 4
	LINC01488	NR_120542.2		n.2809G>C		non_coding_transcript_exon	Exon 6 of 6
	LINC01488	NR_120543.2		n.2666G>C		non_coding_transcript_exon	Exon 5 of 5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01488	ENST00000717996.1	MANE Select	n.1999G>C		non_coding_transcript_exon	Exon 4 of 4
	LINC01488	ENST00000642898.1		n.2603G>C		non_coding_transcript_exon	Exon 7 of 7
	LINC01488	ENST00000644563.1		n.1403G>C		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27682 AN: 152102 Hom.: 2911 Cov.: 33

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.0146

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.143

GnomAD4 exome AF: 0.300 AC: 9 AN: 30 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 5 AN XY: 20

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.333 AC: 2 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.333 AC: 6 AN: 18

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.182 AC: 27700 AN: 152220 Hom.: 2911 Cov.: 33 AF XY: 0.181 AC XY: 13479 AN XY: 74420

African (AFR) AF: 0.275 AC: 11416 AN: 41530

American (AMR) AF: 0.117 AC: 1796 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 541 AN: 3472

East Asian (EAS) AF: 0.0145 AC: 75 AN: 5182

South Asian (SAS) AF: 0.142 AC: 684 AN: 4828

European-Finnish (FIN) AF: 0.179 AC: 1891 AN: 10588

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10865 AN: 68006

Other (OTH) AF: 0.142 AC: 299 AN: 2110

Alfa AF: 0.180 Hom.: 336

Bravo AF: 0.178

Asia WGS AF: 0.105 AC: 367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.54
PhyloP100		0.78

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: rs537626;

hg19: chr11-69307695;