2-38450559-A-G

Variant names:

• chr2-38450559-A-G
• rs6749177
• ENST00000417039.6:n.894+18685T>C

Variant summary

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

The ENST00000417039.6(LINC02613):​n.894+18685T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 152,044 control chromosomes in the GnomAD database, including 17,885 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 0.48 (17885 hom., cov: 33)
• Consequence: LINC02613 ENST00000417039.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.586
• Publications: 3 publications found

Genes affected

LINC02613 (HGNC:54068): (long intergenic non-protein coding RNA 2613)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02613	ENST00000417039.6	n.894+18685T>C		intron_variant	Intron 4 of 4	5
LINC02613	ENST00000658016.1	n.852+18685T>C		intron_variant	Intron 4 of 4
LINC02613	ENST00000659803.1	n.504-1306T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72327 AN: 151926 Hom.: 17854 Cov.: 33

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.476 AC: 72407 AN: 152044 Hom.: 17885 Cov.: 33 AF XY: 0.473 AC XY: 35178 AN XY: 74324

African (AFR) AF: 0.594 AC: 24628 AN: 41474

American (AMR) AF: 0.417 AC: 6369 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1297 AN: 3472

East Asian (EAS) AF: 0.349 AC: 1804 AN: 5168

South Asian (SAS) AF: 0.385 AC: 1853 AN: 4810

European-Finnish (FIN) AF: 0.407 AC: 4295 AN: 10548

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30618 AN: 67970

Other (OTH) AF: 0.484 AC: 1024 AN: 2114

Alfa AF: 0.470 Hom.: 3012

Bravo AF: 0.476

Asia WGS AF: 0.389 AC: 1352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.58
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs6749177; hg19: chr2-38677701;