rs996297

chr13-85433362-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+69267A>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 0.709 in 152,096 control chromosomes in the GnomAD database, including 38,932 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 0.71 (38932 hom., cov: 33)
• Consequence: LINC00351 NR_046989.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.904

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00351	NR_046989.1	n.493+69267A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00351	ENST00000424926.2	n.495+69267A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107692 AN: 151980 Hom.: 38891 Cov.: 33

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.709 AC: 107780 AN: 152096 Hom.: 38932 Cov.: 33 AF XY: 0.702 AC XY: 52169 AN XY: 74336

Gnomad4 AFR AF: 0.844

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.539

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.672

Alfa AF: 0.704 Hom.: 4704

Bravo AF: 0.716

Asia WGS AF: 0.565 AC: 1967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.087
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs996297; hg19: chr13-86007497;