rs1449725

Variant names:

• chr14-38707617-C-T
• rs1449725
• ENST00000776586.1:n.390-7403G>A

Variant summary

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

The ENST00000776586.1(LINC00639):​n.390-7403G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,958 control chromosomes in the GnomAD database, including 10,277 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 (10277 hom., cov: 32)
• Consequence: LINC00639 ENST00000776586.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 2 publications found

Genes affected

LINC00639 (HGNC:27502): (long intergenic non-protein coding RNA 639)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 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
LINC00639	ENST00000776586.1	n.390-7403G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54213 AN: 151840 Hom.: 10266 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.357 AC: 54262 AN: 151958 Hom.: 10277 Cov.: 32 AF XY: 0.359 AC XY: 26662 AN XY: 74278

African (AFR) AF: 0.223 AC: 9250 AN: 41460

American (AMR) AF: 0.382 AC: 5838 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1136 AN: 3468

East Asian (EAS) AF: 0.478 AC: 2466 AN: 5162

South Asian (SAS) AF: 0.436 AC: 2100 AN: 4816

European-Finnish (FIN) AF: 0.417 AC: 4395 AN: 10532

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27853 AN: 67948

Other (OTH) AF: 0.359 AC: 756 AN: 2106

Alfa AF: 0.373 Hom.: 1733

Bravo AF: 0.352

Asia WGS AF: 0.423 AC: 1469 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.32
DANN	Benign	0.76
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1449725; hg19: chr14-39176821;