rs6661746

Positions:

• chr1-8208560-G-A

Variant summary

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

The ENST00000670361.1(LINC01714):​n.239-107G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 151,932 control chromosomes in the GnomAD database, including 5,360 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 (5360 hom., cov: 31)
  • Exomes 𝑓: 0.40 (0 hom.)
• Consequence: LINC01714 ENST00000670361.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.621

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01714	ENST00000670361.1	n.239-107G>A		intron_variant, non_coding_transcript_variant
LINC01714	ENST00000635451.1	n.449-107G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39260 AN: 151804 Hom.: 5357 Cov.: 31

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.252

GnomAD4 exome AF: 0.400 AC: 4 AN: 10 Hom.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.375

GnomAD4 genome AF: 0.258 AC: 39266 AN: 151922 Hom.: 5360 Cov.: 31 AF XY: 0.257 AC XY: 19096 AN XY: 74254

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.253

Alfa AF: 0.273 Hom.: 731

Bravo AF: 0.267

Asia WGS AF: 0.298 AC: 1040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6661746; hg19: chr1-8268620;