rs847498

Variant names:

• chr14-36007471-A-G
• rs847498
• ENST00000550089.2:n.463+8887A>G

Variant summary

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

The ENST00000550089.2(LINC00609):​n.463+8887A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 151,890 control chromosomes in the GnomAD database, including 19,554 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 0.47 (19554 hom., cov: 31)
• Consequence: LINC00609 ENST00000550089.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68
• Publications: 0 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.764 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
LINC00609	ENST00000550089.2	n.463+8887A>G		intron_variant	Intron 3 of 4	3
LINC00609	ENST00000660969.2	n.515+8887A>G		intron_variant	Intron 3 of 3
LINC00609	ENST00000662718.2	n.351+8887A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70700 AN: 151772 Hom.: 19518 Cov.: 31

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.466 AC: 70796 AN: 151890 Hom.: 19554 Cov.: 31 AF XY: 0.463 AC XY: 34344 AN XY: 74208

African (AFR) AF: 0.771 AC: 31957 AN: 41424

American (AMR) AF: 0.351 AC: 5355 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1188 AN: 3470

East Asian (EAS) AF: 0.642 AC: 3301 AN: 5138

South Asian (SAS) AF: 0.473 AC: 2277 AN: 4810

European-Finnish (FIN) AF: 0.285 AC: 3008 AN: 10540

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22275 AN: 67940

Other (OTH) AF: 0.406 AC: 858 AN: 2112

Alfa AF: 0.411 Hom.: 1947

Bravo AF: 0.482

Asia WGS AF: 0.548 AC: 1906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.6
DANN	Benign	0.67
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs847498; hg19: chr14-36476677;