rs2071788

chr6-28944530-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_103538.1(LINC01556):n.747C>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 0.0757 in 222,296 control chromosomes in the GnomAD database, including 817 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 0.071 (481 hom., cov: 32)
  • Exomes 𝑓: 0.086 (336 hom.)
• Consequence: LINC01556 NR_103538.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553

Genes affected

LINC01556 (HGNC:21195): (long intergenic non-protein coding RNA 1556)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.096 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01556	NR_103538.1	n.747C>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01556	ENST00000377186.3	n.459C>T		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.0708 AC: 10774 AN: 152116 Hom.: 481 Cov.: 32

Gnomad AFR AF: 0.0249

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0845

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.0769

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0859

Gnomad OTH AF: 0.0765

GnomAD4 exome AF: 0.0864 AC: 6051 AN: 70062 Hom.: 336 Cov.: 0 AF XY: 0.0839 AC XY: 3206 AN XY: 38226

Gnomad4 AFR exome AF: 0.0258

Gnomad4 AMR exome AF: 0.108

Gnomad4 ASJ exome AF: 0.101

Gnomad4 EAS exome AF: 0.114

Gnomad4 SAS exome AF: 0.0723

Gnomad4 FIN exome AF: 0.111

Gnomad4 NFE exome AF: 0.0879

Gnomad4 OTH exome AF: 0.0854

GnomAD4 genome AF: 0.0708 AC: 10779 AN: 152234 Hom.: 481 Cov.: 32 AF XY: 0.0726 AC XY: 5405 AN XY: 74434

Gnomad4 AFR AF: 0.0249

Gnomad4 AMR AF: 0.0846

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.0772

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0859

Gnomad4 OTH AF: 0.0757

Alfa AF: 0.0817 Hom.: 551

Bravo AF: 0.0705

Asia WGS AF: 0.0660 AC: 230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
Cadd	Benign	0.97
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2071788; hg19: chr6-28912307;