rs6661746

Variant names:

• chr1-8208560-G-A
• rs6661746
• ENST00000452982.2:n.106-107G>A

Variant summary

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

The ENST00000452982.2(LINC01714):​n.106-107G>A variant causes a intron 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 ENST00000452982.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.621
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.364 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.-112G>A		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01714	ENST00000452982.2	TSL:3	n.106-107G>A		intron	N/A
	LINC01714	ENST00000635451.2	TSL:5	n.543-107G>A		intron	N/A
	LINC01714	ENST00000670361.1		n.239-107G>A		intron	N/A

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

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: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.375 AC: 3 AN: 8

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.173 AC: 7151 AN: 41452

American (AMR) AF: 0.372 AC: 5670 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 777 AN: 3470

East Asian (EAS) AF: 0.277 AC: 1427 AN: 5152

South Asian (SAS) AF: 0.292 AC: 1407 AN: 4818

European-Finnish (FIN) AF: 0.234 AC: 2468 AN: 10532

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

European-Non Finnish (NFE) AF: 0.288 AC: 19564 AN: 67960

Other (OTH) AF: 0.253 AC: 535 AN: 2114

Alfa AF: 0.268 Hom.: 738

Bravo AF: 0.267

Asia WGS AF: 0.298 AC: 1040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.57
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs6661746; hg19: chr1-8268620;