rs537626

Positions:

• chr11-69492927-G-C

Variant summary

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

The NR_120542.2(LINC01488):​n.2809G>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 NR_120542.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.782

Genes affected

LINC01488 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01488	NR_120542.2	n.2809G>C		non_coding_transcript_exon_variant	6/6
LINC01488	NR_120543.2	n.2666G>C		non_coding_transcript_exon_variant	5/5
LINC01488	NR_120544.2	n.2705G>C		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01488	ENST00000642898.1	n.2603G>C		non_coding_transcript_exon_variant	7/7
LINC01488	ENST00000644563.1	n.1403G>C		non_coding_transcript_exon_variant	4/4

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

Gnomad4 AFR exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.333

Gnomad4 OTH exome AF: 0.500

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

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.0145

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.142

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs537626; hg19: chr11-69307695;