chr1-189593245-A-G

Variant names:

• chr1-189593245-A-G
• rs463228
• ENST00000758530.1:n.68-10238A>G

Variant summary

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

The ENST00000758530.1(LINC01701):​n.68-10238A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 152,054 control chromosomes in the GnomAD database, including 24,016 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 0.55 (24016 hom., cov: 33)
• Consequence: LINC01701 ENST00000758530.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.557
• Publications: 2 publications found

Genes affected

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

LOC105371657 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.712 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.68-10238A>G		intron	N/A
	LINC01701	ENST00000758531.1		n.160-10238A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83666 AN: 151936 Hom.: 23985 Cov.: 33

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.551 AC: 83743 AN: 152054 Hom.: 24016 Cov.: 33 AF XY: 0.546 AC XY: 40576 AN XY: 74324

African (AFR) AF: 0.719 AC: 29849 AN: 41496

American (AMR) AF: 0.438 AC: 6700 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1640 AN: 3468

East Asian (EAS) AF: 0.456 AC: 2349 AN: 5156

South Asian (SAS) AF: 0.392 AC: 1886 AN: 4816

European-Finnish (FIN) AF: 0.545 AC: 5757 AN: 10558

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.497 AC: 33807 AN: 67958

Other (OTH) AF: 0.522 AC: 1103 AN: 2114

Alfa AF: 0.516 Hom.: 6973

Bravo AF: 0.553

Asia WGS AF: 0.441 AC: 1535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.16
DANN	Benign	0.51
PhyloP100		-0.56

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: rs463228;

hg19: chr1-189562375;

COSMIC: COSV60002318;