rs434052

Variant names:

• chr14-36074442-A-G
• rs434052
• ENST00000546508.1:n.259+3757A>G

Variant summary

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

The ENST00000546508.1(LINC00609):​n.259+3757A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 152,084 control chromosomes in the GnomAD database, including 7,330 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 0.31 (7330 hom., cov: 32)
• Consequence: LINC00609 ENST00000546508.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00609	NR_073454.1	n.259+3757A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00609	ENST00000546508.1	n.259+3757A>G		intron_variant	Intron 1 of 2	3
LINC00609	ENST00000818312.1	n.587+10625A>G		intron_variant	Intron 4 of 6
LINC00609	ENST00000818313.1	n.997+8273A>G		intron_variant	Intron 5 of 9

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46810 AN: 151966 Hom.: 7315 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.308 AC: 46854 AN: 152084 Hom.: 7330 Cov.: 32 AF XY: 0.306 AC XY: 22770 AN XY: 74340

African (AFR) AF: 0.372 AC: 15438 AN: 41506

American (AMR) AF: 0.282 AC: 4300 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 840 AN: 3468

East Asian (EAS) AF: 0.392 AC: 2023 AN: 5164

South Asian (SAS) AF: 0.307 AC: 1480 AN: 4816

European-Finnish (FIN) AF: 0.262 AC: 2760 AN: 10554

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19141 AN: 67984

Other (OTH) AF: 0.304 AC: 643 AN: 2114

Alfa AF: 0.292 Hom.: 802

Bravo AF: 0.315

Asia WGS AF: 0.331 AC: 1149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.45
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs434052; hg19: chr14-36543648;