rs7894765

chr10-123365635-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000662754.1(LINC02641):n.337+4085A>G variant causes a intron, non coding transcript 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 ENST00000662754.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02641	XR_007062326.1	n.8909+3488A>G		intron_variant, non_coding_transcript_variant
LINC02641	XR_002957104.1	n.6362+3488A>G		intron_variant, non_coding_transcript_variant
LINC02641	XR_002957105.1	n.5693+3488A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02641	ENST00000662754.1	n.337+4085A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.386

Alfa AF: 0.334 Hom.: 12113

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7894765; hg19: chr10-125125151;