1-189620209-C-T

Variant names:

• chr1-189620209-C-T
• rs10489759
• ENST00000758530.1:n.265+15054C>T

Variant summary

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

The ENST00000758530.1(LINC01701):​n.265+15054C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 151,770 control chromosomes in the GnomAD database, including 5,425 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 (5425 hom., cov: 32)
• Consequence: LINC01701 ENST00000758530.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.892
• Publications: 3 publications found

Genes affected

LINC01701 (HGNC:52489): (long intergenic non-protein coding RNA 1701)

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 (AFR) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000758530.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01701	ENST00000758530.1		n.265+15054C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24585 AN: 151654 Hom.: 5407 Cov.: 32

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0487

Gnomad EAS AF: 0.00601

Gnomad SAS AF: 0.0364

Gnomad FIN AF: 0.00463

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0212

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.162 AC: 24651 AN: 151770 Hom.: 5425 Cov.: 32 AF XY: 0.158 AC XY: 11699 AN XY: 74168

African (AFR) AF: 0.503 AC: 20810 AN: 41346

American (AMR) AF: 0.109 AC: 1653 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.0487 AC: 169 AN: 3468

East Asian (EAS) AF: 0.00602 AC: 31 AN: 5148

South Asian (SAS) AF: 0.0362 AC: 174 AN: 4806

European-Finnish (FIN) AF: 0.00463 AC: 49 AN: 10578

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0212 AC: 1441 AN: 67916

Other (OTH) AF: 0.144 AC: 303 AN: 2106

Alfa AF: 0.0662 Hom.: 5009

Bravo AF: 0.187

Asia WGS AF: 0.0810 AC: 281 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	0.48
DANN	Benign	0.64
PhyloP100		-0.89

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: rs10489759;

hg19: chr1-189589339;