ENST00000676186.1:n.1779C>T

Variant names:

• chr6-166171188-C-T
• rs7753771
• ENST00000676186.1:n.1779C>T

Variant summary

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

The ENST00000676186.1(LNCDAT):​n.1779C>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 0.159 in 151,918 control chromosomes in the GnomAD database, including 2,795 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 0.16 (2795 hom., cov: 32)
• Consequence: LNCDAT ENST00000676186.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.654
• Publications: 3 publications found

Genes affected

LNCDAT (HGNC:54855): (lncRNA divergent activator of TBXT)

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 (EAS) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LNCDAT	NR_166065.1	n.*16C>T		downstream_gene_variant
LNCDAT	NR_166066.1	n.*16C>T		downstream_gene_variant
LNCDAT	NR_166067.1	n.*16C>T		downstream_gene_variant
LNCDAT	NR_166068.1	n.*16C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LNCDAT	ENST00000676186.1	n.1779C>T		non_coding_transcript_exon_variant	Exon 3 of 3
LNCDAT	ENST00000674611.1	n.*16C>T		downstream_gene_variant
LNCDAT	ENST00000675059.1	n.*209C>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24179 AN: 151800 Hom.: 2799 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.0912

Gnomad ASJ AF: 0.0761

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.0926

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0773

Gnomad OTH AF: 0.138

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.159 AC: 24193 AN: 151918 Hom.: 2795 Cov.: 32 AF XY: 0.161 AC XY: 11990 AN XY: 74270

African (AFR) AF: 0.310 AC: 12837 AN: 41372

American (AMR) AF: 0.0910 AC: 1391 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0761 AC: 264 AN: 3468

East Asian (EAS) AF: 0.399 AC: 2047 AN: 5136

South Asian (SAS) AF: 0.0933 AC: 448 AN: 4800

European-Finnish (FIN) AF: 0.143 AC: 1510 AN: 10562

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0773 AC: 5257 AN: 67978

Other (OTH) AF: 0.140 AC: 295 AN: 2112

Alfa AF: 0.104 Hom.: 3358

Bravo AF: 0.166

Asia WGS AF: 0.239 AC: 832 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.9
DANN	Benign	0.81
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs7753771; hg19: chr6-166584676;