13-111895891-A-G

Variant names:

• chr13-111895891-A-G
• rs7998345
• ENST00000655071.2:n.359+2443A>G

Variant summary

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

The NR_046992.1(LINC00354):​n.71+2443A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 152,202 control chromosomes in the GnomAD database, including 8,880 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 0.33 (8880 hom., cov: 35)
• Consequence: LINC00354 NR_046992.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16
• Publications: 6 publications found

Genes affected

LINC00354 (HGNC:42672): (long intergenic non-protein coding RNA 354)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_046992.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00354	NR_046992.1		n.71+2443A>G		intron	N/A
	LINC00354	NR_120401.1		n.79+2317A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00354	ENST00000655071.2		n.359+2443A>G		intron	N/A
	LINC00354	ENST00000655663.2		n.208+2443A>G		intron	N/A
	LINC00354	ENST00000661311.2		n.1040+939A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.329 AC: 50093 AN: 152086 Hom.: 8877 Cov.: 35

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.329 AC: 50119 AN: 152202 Hom.: 8880 Cov.: 35 AF XY: 0.325 AC XY: 24175 AN XY: 74404

African (AFR) AF: 0.213 AC: 8855 AN: 41530

American (AMR) AF: 0.320 AC: 4894 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1204 AN: 3466

East Asian (EAS) AF: 0.231 AC: 1197 AN: 5180

South Asian (SAS) AF: 0.348 AC: 1681 AN: 4830

European-Finnish (FIN) AF: 0.385 AC: 4089 AN: 10610

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26879 AN: 67976

Other (OTH) AF: 0.343 AC: 726 AN: 2114

Alfa AF: 0.379 Hom.: 6388

Bravo AF: 0.318

Asia WGS AF: 0.256 AC: 887 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.52
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs7998345; hg19: chr13-112550205;