1-8208853-C-T

Variant names:

• chr1-8208853-C-T
• rs6687168
• ENST00000452982.2:n.292C>T

Variant summary

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

The ENST00000452982.2(LINC01714):​n.292C>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 0.259 in 152,048 control chromosomes in the GnomAD database, including 5,396 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 0.26 (5395 hom., cov: 32)
  • Exomes 𝑓: 0.25 (1 hom.)
• Consequence: LINC01714 ENST00000452982.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422
• Publications: 5 publications found

Genes affected

LINC01714 (HGNC:52501): (long intergenic non-protein coding RNA 1714)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000452982.2. 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
	LINC01714	NR_125998.1		n.182C>T		non_coding_transcript_exon	Exon 1 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01714	ENST00000452982.2	TSL:3	n.292C>T		non_coding_transcript_exon	Exon 2 of 5
	LINC01714	ENST00000635451.2	TSL:5	n.729C>T		non_coding_transcript_exon	Exon 2 of 4
	LINC01714	ENST00000670361.1		n.425C>T		non_coding_transcript_exon	Exon 3 of 5

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39373 AN: 151906 Hom.: 5392 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.254

GnomAD4 exome AF: 0.250 AC: 6 AN: 24 Hom.: 1 Cov.: 0 AF XY: 0.143 AC XY: 2 AN XY: 14

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.167 AC: 1 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 4 AN: 16

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

GnomAD4 genome AF: 0.259 AC: 39379 AN: 152024 Hom.: 5395 Cov.: 32 AF XY: 0.258 AC XY: 19135 AN XY: 74284

African (AFR) AF: 0.173 AC: 7190 AN: 41472

American (AMR) AF: 0.373 AC: 5700 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 777 AN: 3472

East Asian (EAS) AF: 0.279 AC: 1438 AN: 5162

South Asian (SAS) AF: 0.292 AC: 1403 AN: 4808

European-Finnish (FIN) AF: 0.235 AC: 2482 AN: 10564

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19583 AN: 67958

Other (OTH) AF: 0.255 AC: 538 AN: 2112

Alfa AF: 0.160 Hom.: 309

Bravo AF: 0.268

Asia WGS AF: 0.299 AC: 1043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.19
DANN	Benign	0.48
PhyloP100		-0.42

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: rs6687168;

hg19: chr1-8268913;