rs9542598

Positions:

• chr13-71157324-A-C

Variant summary

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

The NR_047699.1(LINC00348):​n.160-10046A>C 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 0.471 in 151,964 control chromosomes in the GnomAD database, including 17,786 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 (17786 hom., cov: 32)
• Consequence: LINC00348 NR_047699.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.232

Genes affected

LINC00348 (HGNC:42658): (long intergenic non-protein coding RNA 348)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00348	NR_047699.1	n.160-10046A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00348	ENST00000655045.1	n.424-10046A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71571 AN: 151848 Hom.: 17771 Cov.: 32

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.471 AC: 71623 AN: 151964 Hom.: 17786 Cov.: 32 AF XY: 0.463 AC XY: 34342 AN XY: 74252

Gnomad4 AFR AF: 0.626

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.407

Alfa AF: 0.432 Hom.: 21620

Bravo AF: 0.476

Asia WGS AF: 0.311 AC: 1078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9542598; hg19: chr13-71731456;