5-29387794-T-C

Position:

• chr5-29387794-T-C

Variant summary

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

The NR_104628.1(LINC02064):​n.252+2017A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 151,994 control chromosomes in the GnomAD database, including 13,972 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 (13972 hom., cov: 32)
• Consequence: LINC02064 NR_104628.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960

Genes affected

LINC02064 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02064	NR_104628.1	n.252+2017A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02064	ENST00000506492.6	n.261+2017A>G		intron_variant		5
LINC02064	ENST00000507876.1	n.130+2017A>G		intron_variant		5
LINC02064	ENST00000653940.1	n.124-3402A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64492 AN: 151876 Hom.: 13961 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.425 AC: 64527 AN: 151994 Hom.: 13972 Cov.: 32 AF XY: 0.421 AC XY: 31248 AN XY: 74290

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.454

Alfa AF: 0.457 Hom.: 2003

Bravo AF: 0.416

Asia WGS AF: 0.368 AC: 1281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.3
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9292323; hg19: chr5-29387901;