rs10995195

chr10-62528630-T-C

Variant summary

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

The ENST00000395251.5(LINC02929):n.150+8033T>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 0.18 in 125,678 control chromosomes in the GnomAD database, including 1,797 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 0.18 (1797 hom., cov: 30)
• Consequence: LINC02929 ENST00000395251.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.27

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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.191 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.150+8033T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.180 AC: 22650 AN: 125564 Hom.: 1795 Cov.: 30

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0275

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.157

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.180 AC: 22658 AN: 125678 Hom.: 1797 Cov.: 30 AF XY: 0.182 AC XY: 11075 AN XY: 60986

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.0276

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.180

Alfa AF: 0.165 Hom.: 306

Bravo AF: 0.144

Asia WGS AF: 0.0620 AC: 215 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	14
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10995195; hg19: chr10-64288389;