rs7894765

Variant names:

• chr10-123365635-A-G
• rs7894765
• ENST00000448347.5:n.586+3488A>G

Variant summary

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

The ENST00000448347.5(LINC02641):​n.586+3488A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 152,044 control chromosomes in the GnomAD database, including 11,556 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 0.37 (11556 hom., cov: 33)
• Consequence: LINC02641 ENST00000448347.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.525 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.586+3488A>G		intron	N/A
	LINC02641	ENST00000448671.2	TSL:3	n.538+4085A>G		intron	N/A
	LINC02641	ENST00000656554.1		n.1274+3488A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56865 AN: 151924 Hom.: 11544 Cov.: 33

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.374 AC: 56906 AN: 152044 Hom.: 11556 Cov.: 33 AF XY: 0.367 AC XY: 27304 AN XY: 74304

African (AFR) AF: 0.531 AC: 22030 AN: 41468

American (AMR) AF: 0.304 AC: 4650 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1091 AN: 3468

East Asian (EAS) AF: 0.279 AC: 1445 AN: 5170

South Asian (SAS) AF: 0.238 AC: 1148 AN: 4814

European-Finnish (FIN) AF: 0.272 AC: 2879 AN: 10566

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22478 AN: 67962

Other (OTH) AF: 0.386 AC: 815 AN: 2114

Alfa AF: 0.340 Hom.: 15800

Bravo AF: 0.385

Asia WGS AF: 0.268 AC: 933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.52
PhyloP100		-0.25

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: rs7894765;

hg19: chr10-125125151;