chr10-62526456-A-C

Position:

• chr10-62526456-A-C

Variant summary

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

The ENST00000395251.5(LINC02929):​n.150+5859A>C 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 0.425 in 151,950 control chromosomes in the GnomAD database, including 14,481 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 0.42 (14481 hom., cov: 31)
• Consequence: LINC02929 ENST00000395251.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

Genes affected

LINC02929 (HGNC:55812): (long intergenic non-protein coding RNA 2929)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02929	ENST00000395251.5	n.150+5859A>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64424 AN: 151832 Hom.: 14444 Cov.: 31

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.425 AC: 64528 AN: 151950 Hom.: 14481 Cov.: 31 AF XY: 0.424 AC XY: 31450 AN XY: 74248

Gnomad4 AFR AF: 0.573

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.416

Alfa AF: 0.212 Hom.: 399

Bravo AF: 0.438

Asia WGS AF: 0.388 AC: 1348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.0
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: rs7082733; hg19: chr10-64286215;