2-42975024-G-A

Variant names:

• chr2-42975024-G-A
• rs4640436
• ENST00000705221.1:n.456-2014C>T

Variant summary

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

The ENST00000705221.1(LINC01819):​n.456-2014C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 152,062 control chromosomes in the GnomAD database, including 9,906 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 0.36 (9906 hom., cov: 32)
• Consequence: LINC01819 ENST00000705221.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.51
• Publications: 1 publications found

Genes affected

LINC01819 (HGNC:52624): (long intergenic non-protein coding RNA 1819)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000705221.1. 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
	LINC01819	ENST00000705221.1		n.456-2014C>T		intron	N/A
	LINC01819	ENST00000705222.1		n.773-2014C>T		intron	N/A
	LINC01819	ENST00000705223.1		n.258+1213C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54549 AN: 151944 Hom.: 9902 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.359 AC: 54571 AN: 152062 Hom.: 9906 Cov.: 32 AF XY: 0.356 AC XY: 26483 AN XY: 74332

African (AFR) AF: 0.374 AC: 15515 AN: 41476

American (AMR) AF: 0.288 AC: 4394 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1112 AN: 3468

East Asian (EAS) AF: 0.484 AC: 2498 AN: 5158

South Asian (SAS) AF: 0.426 AC: 2051 AN: 4814

European-Finnish (FIN) AF: 0.322 AC: 3405 AN: 10580

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24280 AN: 67974

Other (OTH) AF: 0.380 AC: 803 AN: 2114

Alfa AF: 0.208 Hom.: 467

Bravo AF: 0.356

Asia WGS AF: 0.415 AC: 1445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.26
DANN	Benign	0.77
PhyloP100		-2.5

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: rs4640436;

hg19: chr2-43202164;