rs61810702

Variant names:

• chr1-115127988-G-A
• rs61810702
• ENST00000820083.1:n.169-4746G>A

Variant summary

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

The ENST00000820083.1(LINC01765):​n.169-4746G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,186 control chromosomes in the GnomAD database, including 6,384 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 0.28 (6384 hom., cov: 33)
• Consequence: LINC01765 ENST00000820083.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192
• Publications: 3 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 = 0.454 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.169-4746G>A		intron	N/A
	LINC01765	ENST00000820084.1		n.*74G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42584 AN: 152070 Hom.: 6383 Cov.: 33

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.280 AC: 42605 AN: 152186 Hom.: 6384 Cov.: 33 AF XY: 0.287 AC XY: 21362 AN XY: 74396

African (AFR) AF: 0.214 AC: 8885 AN: 41522

American (AMR) AF: 0.375 AC: 5730 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1096 AN: 3472

East Asian (EAS) AF: 0.470 AC: 2431 AN: 5174

South Asian (SAS) AF: 0.456 AC: 2202 AN: 4828

European-Finnish (FIN) AF: 0.306 AC: 3236 AN: 10570

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18080 AN: 68012

Other (OTH) AF: 0.288 AC: 609 AN: 2114

Alfa AF: 0.268 Hom.: 1912

Bravo AF: 0.283

Asia WGS AF: 0.403 AC: 1401 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	2.0
DANN	Benign	0.68
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs61810702; hg19: chr1-115670609; COSMIC: COSV59990423;