rs11248532

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000448347.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02641	ENST00000448347.5	TSL:3	n.587-3465A>G		intron	N/A
	LINC02641	ENST00000448671.2	TSL:3	n.539-3465A>G		intron	N/A
	LINC02641	ENST00000655916.1		n.129-3465A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11248532;

hg19: chr10-125205404;