14-35998147-G-C

Variant names:

• chr14-35998147-G-C
• rs17103757
• ENST00000550089.2:n.289-263G>C

Variant summary

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

The ENST00000550089.2(LINC00609):​n.289-263G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0819 in 152,194 control chromosomes in the GnomAD database, including 895 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 0.082 (895 hom., cov: 32)
• Consequence: LINC00609 ENST00000550089.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000550089.2. 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	ENST00000550089.2	TSL:3	n.289-263G>C		intron	N/A
	LINC00609	ENST00000660969.2		n.341-263G>C		intron	N/A
	LINC00609	ENST00000662718.2		n.177-263G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0819 AC: 12457 AN: 152076 Hom.: 892 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.0407

Gnomad AMR AF: 0.0604

Gnomad ASJ AF: 0.0334

Gnomad EAS AF: 0.0942

Gnomad SAS AF: 0.0681

Gnomad FIN AF: 0.0300

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0319

Gnomad OTH AF: 0.0559

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

GnomAD4 genome AF: 0.0819 AC: 12467 AN: 152194 Hom.: 895 Cov.: 32 AF XY: 0.0806 AC XY: 5998 AN XY: 74408

African (AFR) AF: 0.192 AC: 7957 AN: 41484

American (AMR) AF: 0.0603 AC: 922 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0334 AC: 116 AN: 3472

East Asian (EAS) AF: 0.0946 AC: 490 AN: 5178

South Asian (SAS) AF: 0.0677 AC: 326 AN: 4814

European-Finnish (FIN) AF: 0.0300 AC: 318 AN: 10612

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0319 AC: 2171 AN: 68022

Other (OTH) AF: 0.0553 AC: 117 AN: 2114

Alfa AF: 0.0120 Hom.: 4

Bravo AF: 0.0912

Asia WGS AF: 0.105 AC: 365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.65
DANN	Benign	0.61
PhyloP100		-0.057

Splicing

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

Other links and lift over

dbSNP: rs17103757; hg19: chr14-36467353;