rs1146161

Variant names:

• chr1-115116155-A-C
• rs1146161
• ENST00000820083.1:n.168+16404A>C

Variant summary

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

The ENST00000820083.1(LINC01765):​n.168+16404A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,032 control chromosomes in the GnomAD database, including 51,651 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 0.82 (51651 hom., cov: 31)
• Consequence: LINC01765 ENST00000820083.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.832
• Publications: 4 publications found

Genes affected

LINC01765 (HGNC:52555): (long intergenic non-protein coding RNA 1765)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000820083.1. 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
	LINC01765	ENST00000820083.1		n.168+16404A>C		intron	N/A
	LINC01765	ENST00000820084.1		n.165-11512A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125143 AN: 151916 Hom.: 51607 Cov.: 31

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.805

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

GnomAD4 genome AF: 0.824 AC: 125244 AN: 152032 Hom.: 51651 Cov.: 31 AF XY: 0.822 AC XY: 61013 AN XY: 74270

African (AFR) AF: 0.790 AC: 32774 AN: 41468

American (AMR) AF: 0.864 AC: 13203 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2662 AN: 3472

East Asian (EAS) AF: 0.922 AC: 4729 AN: 5130

South Asian (SAS) AF: 0.840 AC: 4045 AN: 4818

European-Finnish (FIN) AF: 0.800 AC: 8449 AN: 10560

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.834 AC: 56705 AN: 67984

Other (OTH) AF: 0.806 AC: 1703 AN: 2112

Alfa AF: 0.828 Hom.: 31100

Bravo AF: 0.830

Asia WGS AF: 0.864 AC: 3008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.32
PhyloP100		-0.83

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: rs1146161;

hg19: chr1-115658776;