chr13-71157324-A-C

Variant names:

• chr13-71157324-A-C
• rs9542598
• ENST00000428761.2:n.256-10046A>C

Variant summary

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

The ENST00000428761.2(LINC00348):​n.256-10046A>C variant causes a intron 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 ENST00000428761.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.232
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC00348	NR_047699.1	n.160-10046A>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00348	ENST00000428761.2	n.256-10046A>C		intron_variant	Intron 2 of 3	3
LINC00348	ENST00000653160.1	n.387-10046A>C		intron_variant	Intron 4 of 5
LINC00348	ENST00000653878.1	n.282-10046A>C		intron_variant	Intron 3 of 4

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

African (AFR) AF: 0.626 AC: 25950 AN: 41440

American (AMR) AF: 0.366 AC: 5590 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1151 AN: 3470

East Asian (EAS) AF: 0.334 AC: 1730 AN: 5182

South Asian (SAS) AF: 0.236 AC: 1138 AN: 4822

European-Finnish (FIN) AF: 0.447 AC: 4706 AN: 10522

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30068 AN: 67952

Other (OTH) AF: 0.407 AC: 859 AN: 2112

Alfa AF: 0.444 Hom.: 53281

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
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs9542598; hg19: chr13-71731456;