rs2282015

Positions:

• chr10-123462521-T-G

Variant summary

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

The ENST00000448347.5(LINC02641):​n.746+13009T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 152,088 control chromosomes in the GnomAD database, including 12,053 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 0.39 (12053 hom., cov: 33)
• Consequence: LINC02641 ENST00000448347.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196

Genes affected

LINC02641 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02641	XR_001747617.3	n.277+13009T>G		intron_variant
LINC02641	XR_001747619.3	n.118-26402T>G		intron_variant
LINC02641	XR_002957104.1	n.6522+13009T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02641	ENST00000448347.5	n.746+13009T>G		intron_variant		3
LINC02641	ENST00000448671.2	n.698+13009T>G		intron_variant		3
LINC02641	ENST00000655916.1	n.288+13009T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.395 AC: 60012 AN: 151970 Hom.: 12040 Cov.: 33

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.395 AC: 60063 AN: 152088 Hom.: 12053 Cov.: 33 AF XY: 0.395 AC XY: 29354 AN XY: 74362

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.412

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.432

Alfa AF: 0.392 Hom.: 16442

Bravo AF: 0.408

Asia WGS AF: 0.398 AC: 1382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	13
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2282015; hg19: chr10-125222037;