13-42346817-T-C

Variant names:

• chr13-42346817-T-C
• rs912100
• ENST00000637462.1:n.229+4215T>C

Variant summary

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

The ENST00000637462.1(LINC02341):​n.229+4215T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,176 control chromosomes in the GnomAD database, including 6,609 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 0.28 (6609 hom., cov: 32)
• Consequence: LINC02341 ENST00000637462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442
• Publications: 7 publications found

Genes affected

LINC02341 (HGNC:53261): (long intergenic non-protein coding RNA 2341)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637462.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02341	ENST00000637462.1	TSL:5	n.229+4215T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42475 AN: 152058 Hom.: 6609 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.279 AC: 42475 AN: 152176 Hom.: 6609 Cov.: 32 AF XY: 0.279 AC XY: 20773 AN XY: 74406

African (AFR) AF: 0.156 AC: 6466 AN: 41530

American (AMR) AF: 0.297 AC: 4536 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 736 AN: 3468

East Asian (EAS) AF: 0.131 AC: 680 AN: 5184

South Asian (SAS) AF: 0.255 AC: 1229 AN: 4826

European-Finnish (FIN) AF: 0.393 AC: 4161 AN: 10584

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23690 AN: 67986

Other (OTH) AF: 0.260 AC: 548 AN: 2110

Alfa AF: 0.301 Hom.: 7095

Bravo AF: 0.266

Asia WGS AF: 0.212 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.61
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs912100; hg19: chr13-42920953;