ENST00000448347.5:n.587-3465A>G

Variant names:

• chr10-123445888-A-G
• rs11248532
• ENST00000448347.5:n.587-3465A>G

Variant summary

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

The ENST00000448347.5(LINC02641):​n.587-3465A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,240 control chromosomes in the GnomAD database, including 4,448 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 0.23 (4448 hom., cov: 33)
• Consequence: LINC02641 ENST00000448347.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230
• Publications: 0 publications found

Genes affected

LINC02641 (HGNC:54125): (long intergenic non-protein coding RNA 2641)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02641	XR_001747617.3	n.118-3465A>G		intron_variant	Intron 1 of 6
LINC02641	XR_001747619.3	n.117+16718A>G		intron_variant	Intron 1 of 5
LINC02641	XR_002957104.1	n.6363-3465A>G		intron_variant	Intron 4 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02641	ENST00000448347.5	n.587-3465A>G		intron_variant	Intron 3 of 4	3
LINC02641	ENST00000448671.2	n.539-3465A>G		intron_variant	Intron 3 of 4	3
LINC02641	ENST00000655916.1	n.129-3465A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35588 AN: 152122 Hom.: 4445 Cov.: 33

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.0792

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.234 AC: 35624 AN: 152240 Hom.: 4448 Cov.: 33 AF XY: 0.230 AC XY: 17133 AN XY: 74422

African (AFR) AF: 0.298 AC: 12382 AN: 41534

American (AMR) AF: 0.194 AC: 2972 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 640 AN: 3472

East Asian (EAS) AF: 0.125 AC: 647 AN: 5180

South Asian (SAS) AF: 0.0788 AC: 381 AN: 4832

European-Finnish (FIN) AF: 0.255 AC: 2702 AN: 10600

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15302 AN: 68004

Other (OTH) AF: 0.218 AC: 461 AN: 2116

Alfa AF: 0.224 Hom.: 6058

Bravo AF: 0.234

Asia WGS AF: 0.126 AC: 437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.80
DANN	Benign	0.18
PhyloP100		-0.023

Splicing

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

Other links and lift over

dbSNP: rs11248532; hg19: chr10-125205404;