1-189645191-A-T

Variant names:

• chr1-189645191-A-T
• rs487616
• ENST00000758530.1:n.265+40036A>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+40036A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 151,782 control chromosomes in the GnomAD database, including 18,003 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 0.48 (18003 hom., cov: 31)
• Consequence: LINC01701 ENST00000758530.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.535 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+40036A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73282 AN: 151668 Hom.: 17985 Cov.: 31

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.483 AC: 73345 AN: 151782 Hom.: 18003 Cov.: 31 AF XY: 0.479 AC XY: 35539 AN XY: 74146

African (AFR) AF: 0.541 AC: 22360 AN: 41354

American (AMR) AF: 0.373 AC: 5689 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1491 AN: 3468

East Asian (EAS) AF: 0.453 AC: 2323 AN: 5128

South Asian (SAS) AF: 0.363 AC: 1738 AN: 4794

European-Finnish (FIN) AF: 0.526 AC: 5531 AN: 10516

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32602 AN: 67950

Other (OTH) AF: 0.456 AC: 962 AN: 2108

Alfa AF: 0.355 Hom.: 965

Bravo AF: 0.475

Asia WGS AF: 0.406 AC: 1415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.33
PhyloP100		-0.35

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: rs487616;

hg19: chr1-189614321;

COSMIC: COSV60002565;