rs727243

Variant names:

• chr13-42421126-G-A
• rs727243
• ENST00000637462.1:n.868+9074G>A

Variant summary

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

The ENST00000637462.1(LINC02341):​n.868+9074G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,114 control chromosomes in the GnomAD database, including 3,405 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 0.21 (3405 hom., cov: 32)
• Consequence: LINC02341 ENST00000637462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.284 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.868+9074G>A		intron_variant	Intron 5 of 7	5

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31624 AN: 151996 Hom.: 3392 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.208 AC: 31660 AN: 152114 Hom.: 3405 Cov.: 32 AF XY: 0.207 AC XY: 15397 AN XY: 74378

African (AFR) AF: 0.178 AC: 7396 AN: 41482

American (AMR) AF: 0.164 AC: 2500 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 973 AN: 3470

East Asian (EAS) AF: 0.214 AC: 1104 AN: 5170

South Asian (SAS) AF: 0.297 AC: 1429 AN: 4816

European-Finnish (FIN) AF: 0.205 AC: 2166 AN: 10576

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15332 AN: 67994

Other (OTH) AF: 0.210 AC: 443 AN: 2112

Alfa AF: 0.201 Hom.: 523

Bravo AF: 0.201

Asia WGS AF: 0.285 AC: 989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.50
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs727243; hg19: chr13-42995262;