rs1755774

Variant names:

• chr14-36219310-A-G
• rs1755774
• ENST00000556542.2:n.2001+3795A>G

Variant summary

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

The ENST00000556542.2(LINC00609):​n.2001+3795A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 151,958 control chromosomes in the GnomAD database, including 7,003 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 0.30 (7003 hom., cov: 32)
• Consequence: LINC00609 ENST00000556542.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.665
• Publications: 4 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000556542.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00609	ENST00000556542.2	TSL:4	n.2001+3795A>G		intron	N/A
	LINC00609	ENST00000818312.1		n.835-16014A>G		intron	N/A
	LINC00609	ENST00000818313.1		n.1486+3795A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45713 AN: 151840 Hom.: 6987 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.301 AC: 45759 AN: 151958 Hom.: 7003 Cov.: 32 AF XY: 0.301 AC XY: 22326 AN XY: 74274

African (AFR) AF: 0.248 AC: 10298 AN: 41484

American (AMR) AF: 0.297 AC: 4530 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1248 AN: 3468

East Asian (EAS) AF: 0.380 AC: 1961 AN: 5160

South Asian (SAS) AF: 0.460 AC: 2213 AN: 4814

European-Finnish (FIN) AF: 0.263 AC: 2783 AN: 10564

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.319 AC: 21646 AN: 67918

Other (OTH) AF: 0.326 AC: 688 AN: 2108

Alfa AF: 0.298 Hom.: 1175

Bravo AF: 0.299

Asia WGS AF: 0.426 AC: 1476 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.66
PhyloP100		-0.67

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1755774;

hg19: chr14-36688516;