5-164297275-A-G

Position:

• chr5-164297275-A-G

Variant summary

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

The ENST00000519570.5(LINC03000):​n.219+79A>G 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 0.204 in 151,944 control chromosomes in the GnomAD database, including 3,308 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 0.20 (3308 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC03000 ENST00000519570.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

Genes affected

LINC03000 (HGNC:56116): (long intergenic non-protein coding RNA 3000)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC03000	XR_001742489.2	n.492+79A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03000	ENST00000519570.5	n.219+79A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30968 AN: 151826 Hom.: 3305 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.204 AC: 30974 AN: 151944 Hom.: 3308 Cov.: 32 AF XY: 0.206 AC XY: 15271 AN XY: 74270

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.186

Alfa AF: 0.181 Hom.: 1378

Bravo AF: 0.211

Asia WGS AF: 0.178 AC: 617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.7
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2964911; hg19: chr5-163724281;