rs6703780

chr1-101689492-G-Achr1-101689492-G-Cchr1-101689492-G-T

Variant summary

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

The NR_183474.1(LINC01709):n.230-34250G>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 0.163 in 152,136 control chromosomes in the GnomAD database, including 5,714 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 (5714 hom., cov: 32)
• Consequence: LINC01709 NR_183474.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.81

Genes affected

LINC01709 (HGNC:52497): (long intergenic non-protein coding RNA 1709)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01709	NR_183474.1	n.230-34250G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01709	ENST00000657394.1	n.138-34250G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24717 AN: 152020 Hom.: 5675 Cov.: 32

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0742

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.0177

Gnomad SAS AF: 0.0928

Gnomad FIN AF: 0.00264

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0170

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.163 AC: 24821 AN: 152136 Hom.: 5714 Cov.: 32 AF XY: 0.159 AC XY: 11808 AN XY: 74380

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.0742

Gnomad4 ASJ AF: 0.0519

Gnomad4 EAS AF: 0.0177

Gnomad4 SAS AF: 0.0925

Gnomad4 FIN AF: 0.00264

Gnomad4 NFE AF: 0.0170

Gnomad4 OTH AF: 0.134

Alfa AF: 0.00686 Hom.: 13

Bravo AF: 0.181

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.12
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6703780; hg19: chr1-102155048;