rs12451840

Positions:

• chr17-73811574-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_027146.1(LINC00469):​n.228+12114A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0423 in 152,028 control chromosomes in the GnomAD database, including 276 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 0.042 (276 hom., cov: 32)
• Consequence: LINC00469 NR_027146.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.457

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00469	NR_027146.1	n.228+12114A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00469	ENST00000321800.11	n.211+12114A>G		intron_variant, non_coding_transcript_variant		1
LINC00469	ENST00000544677.1	n.211+12114A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0422 AC: 6406 AN: 151910 Hom.: 269 Cov.: 32

Gnomad AFR AF: 0.0103

Gnomad AMI AF: 0.0857

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0139

Gnomad FIN AF: 0.0418

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0456

Gnomad OTH AF: 0.0379

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

GnomAD4 genome AF: 0.0423 AC: 6424 AN: 152028 Hom.: 276 Cov.: 32 AF XY: 0.0443 AC XY: 3293 AN XY: 74290

Gnomad4 AFR AF: 0.0103

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.0242

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0142

Gnomad4 FIN AF: 0.0418

Gnomad4 NFE AF: 0.0456

Gnomad4 OTH AF: 0.0375

Alfa AF: 0.0455 Hom.: 37

Bravo AF: 0.0479

Asia WGS AF: 0.0160 AC: 54 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12451840; hg19: chr17-71807713;