10-62622902-G-A

Position:

• chr10-62622902-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000395251.5(LINC02929):​n.151-20840G>A 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 0.142 in 150,264 control chromosomes in the GnomAD database, including 1,741 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.14 (1741 hom., cov: 31)
• Consequence: LINC02929 ENST00000395251.5 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.04

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 10-62622902-G-A is Benign according to our data. Variant chr10-62622902-G-A is described in ClinVar as [Benign]. Clinvar id is 1266745.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.174 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.151-20840G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21347 AN: 150142 Hom.: 1740 Cov.: 31

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.0897

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.0146

Gnomad SAS AF: 0.0570

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.142 AC: 21368 AN: 150264 Hom.: 1741 Cov.: 31 AF XY: 0.140 AC XY: 10236 AN XY: 73310

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.0896

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.0147

Gnomad4 SAS AF: 0.0574

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.123

Alfa AF: 0.167 Hom.: 281

Bravo AF: 0.132

Asia WGS AF: 0.0620 AC: 218 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 17, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.83
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12774545; hg19: chr10-64382662;