rs7998345

Positions:

• chr13-111895891-A-G

Variant summary

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

The NR_046992.1(LINC00354):​n.71+2443A>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 0.329 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00354	NR_046992.1	n.71+2443A>G		intron_variant, non_coding_transcript_variant
LINC00354	NR_120401.1	n.79+2317A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00354	ENST00000663211.1	n.248-4098A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.343

Alfa AF: 0.378 Hom.: 5811

Bravo AF: 0.318

Asia WGS AF: 0.256 AC: 887 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7998345; hg19: chr13-112550205;