ENST00000419745.1:n.564-547A>G

Variant names:

• chr3-186812695-T-C
• rs266717
• ENST00000419745.1:n.564-547A>G

Variant summary

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

The ENST00000419745.1(LINC02043):​n.564-547A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 151,826 control chromosomes in the GnomAD database, including 25,030 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 (25030 hom., cov: 31)
• Consequence: LINC02043 ENST00000419745.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 34 publications found

Genes affected

LINC02043 (HGNC:52883): (long intergenic non-protein coding RNA 2043)

ENSG00000231724 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02043	NR_125409.1	n.564-547A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02043	ENST00000419745.1	n.564-547A>G		intron_variant	Intron 3 of 3	2
ENSG00000231724	ENST00000434957.1	n.195+4809T>C		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86111 AN: 151708 Hom.: 24991 Cov.: 31

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.568 AC: 86205 AN: 151826 Hom.: 25030 Cov.: 31 AF XY: 0.572 AC XY: 42445 AN XY: 74208

African (AFR) AF: 0.670 AC: 27727 AN: 41370

American (AMR) AF: 0.532 AC: 8118 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1592 AN: 3468

East Asian (EAS) AF: 0.544 AC: 2803 AN: 5148

South Asian (SAS) AF: 0.495 AC: 2381 AN: 4812

European-Finnish (FIN) AF: 0.696 AC: 7335 AN: 10544

Middle Eastern (MID) AF: 0.401 AC: 117 AN: 292

European-Non Finnish (NFE) AF: 0.509 AC: 34562 AN: 67922

Other (OTH) AF: 0.497 AC: 1049 AN: 2110

Alfa AF: 0.521 Hom.: 73707

Bravo AF: 0.558

Asia WGS AF: 0.566 AC: 1968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.21
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs266717; hg19: chr3-186530484;