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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02641	XR_002957104.1	n.6362+3488A>G		intron_variant	Intron 4 of 9
LINC02641	XR_002957105.1	n.5693+3488A>G		intron_variant	Intron 3 of 8
LINC02641	XR_007062326.1	n.8909+3488A>G		intron_variant	Intron 6 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02641	ENST00000448347.5	n.586+3488A>G		intron_variant	Intron 3 of 4	3
LINC02641	ENST00000448671.2	n.538+4085A>G		intron_variant	Intron 3 of 4	3
LINC02641	ENST00000656554.1	n.1274+3488A>G		intron_variant	Intron 4 of 5

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 v4.3

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

Other links and lift over

dbSNP: rs7894765; hg19: chr10-125125151;