17-73769434-C-T

Variant names:

• chr17-73769434-C-T
• rs1947825
• ENST00000321800.11:n.212-8408G>A

Variant summary

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

The ENST00000321800.11(LINC00469):​n.212-8408G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 151,232 control chromosomes in the GnomAD database, including 17,271 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 0.46 (17271 hom., cov: 31)
• Consequence: LINC00469 ENST00000321800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0530
• Publications: 1 publications found

Genes affected

LINC00469 (HGNC:26863): (long intergenic non-protein coding RNA 469)

LINC02092 (HGNC:52943): (long intergenic non-protein coding RNA 2092)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00469	NR_027146.1	n.229-8408G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00469	ENST00000321800.11	n.212-8408G>A		intron_variant	Intron 2 of 3	1
LINC00469	ENST00000544677.2	n.212-8408G>A		intron_variant	Intron 2 of 3	1
LINC00469	ENST00000579749.2	n.560+6764G>A		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.463 AC: 69985 AN: 151120 Hom.: 17265 Cov.: 31

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.463 AC: 70020 AN: 151232 Hom.: 17271 Cov.: 31 AF XY: 0.474 AC XY: 35031 AN XY: 73940

African (AFR) AF: 0.286 AC: 11627 AN: 40716

American (AMR) AF: 0.503 AC: 7672 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1783 AN: 3460

East Asian (EAS) AF: 0.641 AC: 3305 AN: 5160

South Asian (SAS) AF: 0.531 AC: 2557 AN: 4816

European-Finnish (FIN) AF: 0.658 AC: 6957 AN: 10566

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.511 AC: 34697 AN: 67938

Other (OTH) AF: 0.494 AC: 1039 AN: 2104

Alfa AF: 0.494 Hom.: 17317

Bravo AF: 0.443

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.5
DANN	Benign	0.45
PhyloP100		0.053

Splicing

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

Other links and lift over

dbSNP: rs1947825; hg19: chr17-71765573;