rs9301064

Variant names:

• chr13-105751338-G-C
• rs9301064
• ENST00000415294.3:n.887-9925G>C

Variant summary

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

The ENST00000415294.3(LINC00343):​n.887-9925G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 151,990 control chromosomes in the GnomAD database, including 19,457 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 0.47 (19457 hom., cov: 31)
• Consequence: LINC00343 ENST00000415294.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169
• Publications: 1 publications found

Genes affected

LINC00343 (HGNC:42500): (long intergenic non-protein coding RNA 343)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00343	NR_046391.2	n.743-9925G>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00343	ENST00000415294.3	n.887-9925G>C		intron_variant	Intron 3 of 4	5
LINC00343	ENST00000454555.2	n.928-9925G>C		intron_variant	Intron 3 of 3	2
LINC00343	ENST00000598229.2	n.195-9925G>C		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70733 AN: 151872 Hom.: 19456 Cov.: 31

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.465 AC: 70732 AN: 151990 Hom.: 19457 Cov.: 31 AF XY: 0.470 AC XY: 34907 AN XY: 74278

African (AFR) AF: 0.150 AC: 6215 AN: 41452

American (AMR) AF: 0.542 AC: 8279 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2023 AN: 3470

East Asian (EAS) AF: 0.624 AC: 3229 AN: 5172

South Asian (SAS) AF: 0.577 AC: 2776 AN: 4810

European-Finnish (FIN) AF: 0.598 AC: 6309 AN: 10558

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.590 AC: 40080 AN: 67942

Other (OTH) AF: 0.497 AC: 1051 AN: 2114

Alfa AF: 0.511 Hom.: 2719

Bravo AF: 0.447

Asia WGS AF: 0.560 AC: 1948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.66
DANN	Benign	0.44
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs9301064; hg19: chr13-106403687;