2-15750796-C-G

Variant names:

• chr2-15750796-C-G
• rs10460289
• ENST00000770646.1:n.529-32351C>G

Variant summary

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

The ENST00000770646.1(LINC01804):​n.529-32351C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 152,134 control chromosomes in the GnomAD database, including 25,404 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 0.57 (25404 hom., cov: 33)
• Consequence: LINC01804 ENST00000770646.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.498
• Publications: 3 publications found

Genes affected

LINC01804 (HGNC:52596): (long intergenic non-protein coding RNA 1804)

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 (AMR) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000770646.1. 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
	LINC01804	ENST00000770646.1		n.529-32351C>G		intron	N/A
	LINC01804	ENST00000770647.1		n.407-32351C>G		intron	N/A
	LINC01804	ENST00000770648.1		n.430-30808C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.573 AC: 87108 AN: 152016 Hom.: 25394 Cov.: 33

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.573 AC: 87167 AN: 152134 Hom.: 25404 Cov.: 33 AF XY: 0.575 AC XY: 42747 AN XY: 74364

African (AFR) AF: 0.491 AC: 20368 AN: 41496

American (AMR) AF: 0.712 AC: 10886 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2076 AN: 3470

East Asian (EAS) AF: 0.658 AC: 3404 AN: 5174

South Asian (SAS) AF: 0.382 AC: 1844 AN: 4824

European-Finnish (FIN) AF: 0.594 AC: 6270 AN: 10560

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.592 AC: 40283 AN: 68002

Other (OTH) AF: 0.623 AC: 1313 AN: 2108

Alfa AF: 0.445 Hom.: 1187

Bravo AF: 0.584

Asia WGS AF: 0.530 AC: 1843 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	0.64
DANN	Benign	0.74
PhyloP100		-0.50

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: rs10460289;

hg19: chr2-15890920;