13-42443334-T-C

Variant names:

• chr13-42443334-T-C
• rs7316953
• ENST00000637043.2:n.336+5862T>C

Variant summary

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

The ENST00000637043.2(LINC02341):​n.336+5862T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.781 in 152,124 control chromosomes in the GnomAD database, including 46,541 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 0.78 (46541 hom., cov: 31)
• Consequence: LINC02341 ENST00000637043.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280
• Publications: 8 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02341	NR_135319.1	n.336+5862T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02341	ENST00000637043.2	n.336+5862T>C		intron_variant	Intron 3 of 3	3
LINC02341	ENST00000637462.1	n.1118-633T>C		intron_variant	Intron 7 of 7	5
LINC02341	ENST00000765075.1	n.349-633T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118777 AN: 152008 Hom.: 46497 Cov.: 31

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.787

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

GnomAD4 genome AF: 0.781 AC: 118870 AN: 152124 Hom.: 46541 Cov.: 31 AF XY: 0.783 AC XY: 58221 AN XY: 74376

African (AFR) AF: 0.795 AC: 32976 AN: 41490

American (AMR) AF: 0.828 AC: 12662 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.716 AC: 2487 AN: 3472

East Asian (EAS) AF: 0.785 AC: 4061 AN: 5176

South Asian (SAS) AF: 0.696 AC: 3356 AN: 4822

European-Finnish (FIN) AF: 0.795 AC: 8407 AN: 10580

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.771 AC: 52381 AN: 67976

Other (OTH) AF: 0.784 AC: 1655 AN: 2110

Alfa AF: 0.770 Hom.: 24540

Bravo AF: 0.788

Asia WGS AF: 0.715 AC: 2488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.8
DANN	Benign	0.70
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs7316953; hg19: chr13-43017470;