chr14-36104812-C-T

Variant names:

• chr14-36104812-C-T
• rs1537424
• ENST00000546508.1:n.259+34127C>T

Variant summary

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

The ENST00000546508.1(LINC00609):​n.259+34127C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 152,004 control chromosomes in the GnomAD database, including 19,692 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 0.49 (19692 hom., cov: 33)
• Consequence: LINC00609 ENST00000546508.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 26 publications found

Genes affected

LINC00609 (HGNC:43960): (long intergenic non-protein coding RNA 609)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00609	NR_073454.1	n.259+34127C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00609	ENST00000546508.1	n.259+34127C>T		intron_variant	Intron 1 of 2	3
LINC00609	ENST00000818312.1	n.587+40995C>T		intron_variant	Intron 4 of 6
LINC00609	ENST00000818313.1	n.997+38643C>T		intron_variant	Intron 5 of 9

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75175 AN: 151886 Hom.: 19692 Cov.: 33

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.495 AC: 75191 AN: 152004 Hom.: 19692 Cov.: 33 AF XY: 0.498 AC XY: 36968 AN XY: 74284

African (AFR) AF: 0.311 AC: 12893 AN: 41452

American (AMR) AF: 0.501 AC: 7650 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1723 AN: 3470

East Asian (EAS) AF: 0.474 AC: 2448 AN: 5170

South Asian (SAS) AF: 0.539 AC: 2596 AN: 4814

European-Finnish (FIN) AF: 0.618 AC: 6521 AN: 10544

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39652 AN: 67966

Other (OTH) AF: 0.504 AC: 1065 AN: 2114

Alfa AF: 0.555 Hom.: 105075

Bravo AF: 0.478

Asia WGS AF: 0.485 AC: 1688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.80
DANN	Benign	0.38
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1537424; hg19: chr14-36574018;