10-62620576-T-C

Variant summary

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

The ENST00000395251.5(LINC02929):n.151-23166T>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 0.673 in 152,162 control chromosomes in the GnomAD database, including 36,072 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 0.67 (36072 hom., cov: 33)
• Consequence: LINC02929 ENST00000395251.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.02

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02929	ENST00000395251.5	n.151-23166T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102287 AN: 152044 Hom.: 36010 Cov.: 33

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.673 AC: 102422 AN: 152162 Hom.: 36072 Cov.: 33 AF XY: 0.677 AC XY: 50376 AN XY: 74386

Gnomad4 AFR AF: 0.875

Gnomad4 AMR AF: 0.678

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.557

Gnomad4 FIN AF: 0.723

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.624

Alfa AF: 0.575 Hom.: 38502

Bravo AF: 0.677

Asia WGS AF: 0.597 AC: 2077 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	0.14
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2393903; hg19: chr10-64380336;