rs845086

Variant names:

• chr10-123454284-A-C
• rs845086
• ENST00000448347.5:n.746+4772A>C

Your query was ambiguous. Multiple possible variants found:

• chr10-123454284-A-C
• chr10-123454284-A-T

Variant summary

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

The ENST00000448347.5(LINC02641):​n.746+4772A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 152,028 control chromosomes in the GnomAD database, including 20,057 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 0.49 (20057 hom., cov: 32)
• Consequence: LINC02641 ENST00000448347.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 1 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.589 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.746+4772A>C		intron	N/A
	LINC02641	ENST00000448671.2	TSL:3	n.698+4772A>C		intron	N/A
	LINC02641	ENST00000655916.1		n.288+4772A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74978 AN: 151910 Hom.: 20046 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.493 AC: 75006 AN: 152028 Hom.: 20057 Cov.: 32 AF XY: 0.494 AC XY: 36696 AN XY: 74308

African (AFR) AF: 0.272 AC: 11273 AN: 41468

American (AMR) AF: 0.550 AC: 8388 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.524 AC: 1817 AN: 3470

East Asian (EAS) AF: 0.545 AC: 2819 AN: 5176

South Asian (SAS) AF: 0.460 AC: 2217 AN: 4816

European-Finnish (FIN) AF: 0.609 AC: 6430 AN: 10558

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40326 AN: 67962

Other (OTH) AF: 0.522 AC: 1104 AN: 2114

Alfa AF: 0.546 Hom.: 4764

Bravo AF: 0.481

Asia WGS AF: 0.529 AC: 1841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.4
DANN	Benign	0.60
PhyloP100		0.078

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: rs845086; hg19: chr10-125213800;