13-42346817-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02341	ENST00000637462.1	n.229+4215T>C		intron_variant	Intron 2 of 7	5

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

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.260

Alfa AF: 0.310 Hom.: 4799

Bravo AF: 0.266

Asia WGS AF: 0.212 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs912100; hg19: chr13-42920953;