rs2071788

Variant names:

• chr6-28944530-C-T
• rs2071788
• ENST00000377186.4:n.619C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000377186.4(LINC01556):​n.619C>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 ENST00000377186.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553
• Publications: 14 publications found

Genes affected

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

TRM-CAT3-1 (HGNC:34779):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC01556	NR_103538.1	n.747C>T		non_coding_transcript_exon_variant	Exon 1 of 1
TRM-CAT3-1	unassigned_transcript_1086	c.-45C>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01556	ENST00000377186.4	n.619C>T		non_coding_transcript_exon_variant	Exon 2 of 2	2
LINC01556	ENST00000824165.1	n.722C>T		non_coding_transcript_exon_variant	Exon 3 of 3
LINC01556	ENST00000824166.1	n.915C>T		non_coding_transcript_exon_variant	Exon 5 of 5

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

African (AFR) AF: 0.0258 AC: 71 AN: 2748

American (AMR) AF: 0.108 AC: 540 AN: 4988

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 161 AN: 1588

East Asian (EAS) AF: 0.114 AC: 453 AN: 3986

South Asian (SAS) AF: 0.0723 AC: 935 AN: 12932

European-Finnish (FIN) AF: 0.111 AC: 293 AN: 2636

Middle Eastern (MID) AF: 0.0214 AC: 5 AN: 234

European-Non Finnish (NFE) AF: 0.0879 AC: 3313 AN: 37672

Other (OTH) AF: 0.0854 AC: 280 AN: 3278

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

African (AFR) AF: 0.0249 AC: 1033 AN: 41554

American (AMR) AF: 0.0846 AC: 1293 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 364 AN: 3468

East Asian (EAS) AF: 0.103 AC: 535 AN: 5182

South Asian (SAS) AF: 0.0772 AC: 372 AN: 4820

European-Finnish (FIN) AF: 0.107 AC: 1133 AN: 10592

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0859 AC: 5842 AN: 68010

Other (OTH) AF: 0.0757 AC: 160 AN: 2114

Alfa AF: 0.0785 Hom.: 987

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
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs2071788; hg19: chr6-28912307;