rs9319160

Variant names:

• chr13-85446510-A-G
• rs9319160
• ENST00000424926.2:n.495+82415A>G

Variant summary

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

The ENST00000424926.2(LINC00351):​n.495+82415A>G variant causes a intron 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 ENST00000424926.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC00351	NR_046989.1	n.493+82415A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00351	ENST00000424926.2	n.495+82415A>G		intron_variant	Intron 1 of 3	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

African (AFR) AF: 0.142 AC: 5890 AN: 41470

American (AMR) AF: 0.316 AC: 4800 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1852 AN: 3454

East Asian (EAS) AF: 0.432 AC: 2228 AN: 5152

South Asian (SAS) AF: 0.490 AC: 2360 AN: 4816

European-Finnish (FIN) AF: 0.368 AC: 3869 AN: 10524

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.335 AC: 22636 AN: 67518

Other (OTH) AF: 0.331 AC: 693 AN: 2094

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
PhyloP100		-0.079

Splicing

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

Other links and lift over

dbSNP: rs9319160; hg19: chr13-86020645;