rs9319160

chr13-85446510-A-G

Variant summary

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

The NR_046989.1(LINC00351):n.493+82415A>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 0.296 in 151,408 control chromosomes in the GnomAD database, including 7,521 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 (7521 hom., cov: 31)
• Consequence: LINC00351 NR_046989.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790

Genes affected

LINC00351 (HGNC:42669): (long intergenic non-protein coding RNA 351)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00351	NR_046989.1	n.493+82415A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00351	ENST00000424926.2	n.495+82415A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44786 AN: 151286 Hom.: 7509 Cov.: 31

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.365

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.296 AC: 44819 AN: 151408 Hom.: 7521 Cov.: 31 AF XY: 0.303 AC XY: 22440 AN XY: 73958

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.331

Alfa AF: 0.310 Hom.: 947

Bravo AF: 0.285

Asia WGS AF: 0.435 AC: 1503 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.4
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9319160; hg19: chr13-86020645;