rs9525625

Variant names:

• chr13-42443894-T-C
• rs9525625
• ENST00000637043.2:n.336+6422T>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+6422T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 152,088 control chromosomes in the GnomAD database, including 16,010 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 0.44 (16010 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC02341 ENST00000637043.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 22 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02341	NR_135319.1	n.336+6422T>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+6422T>C		intron_variant	Intron 3 of 3	3
LINC02341	ENST00000637462.1	n.1118-73T>C		intron_variant	Intron 7 of 7	5
LINC02341	ENST00000765075.1	n.349-73T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67532 AN: 151970 Hom.: 16010 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.444 AC: 67543 AN: 152088 Hom.: 16010 Cov.: 32 AF XY: 0.447 AC XY: 33260 AN XY: 74348

African (AFR) AF: 0.308 AC: 12778 AN: 41484

American (AMR) AF: 0.416 AC: 6359 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1474 AN: 3470

East Asian (EAS) AF: 0.194 AC: 1006 AN: 5174

South Asian (SAS) AF: 0.457 AC: 2204 AN: 4818

European-Finnish (FIN) AF: 0.617 AC: 6523 AN: 10568

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35651 AN: 67970

Other (OTH) AF: 0.435 AC: 920 AN: 2114

Alfa AF: 0.455 Hom.: 5644

Bravo AF: 0.422

Asia WGS AF: 0.324 AC: 1129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.9
DANN	Benign	0.51
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs9525625; hg19: chr13-43018030;