chr5-164445062-T-G

Position:

• chr5-164445062-T-G

Variant summary

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

The ENST00000486913.3(LINC03000):​n.86-41607T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,052 control chromosomes in the GnomAD database, including 7,570 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 0.30 (7570 hom., cov: 32)
• Consequence: LINC03000 ENST00000486913.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441

Genes affected

LINC03000 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC03000	XR_001742489.2	n.576+90838T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC03000	ENST00000486913.3	n.86-41607T>G		intron_variant		2
LINC03000	ENST00000517508.5	n.586-41607T>G		intron_variant		4
LINC03000	ENST00000519329.2	n.316-41612T>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45486 AN: 151934 Hom.: 7547 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.300 AC: 45553 AN: 152052 Hom.: 7570 Cov.: 32 AF XY: 0.301 AC XY: 22375 AN XY: 74330

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.318

Alfa AF: 0.119 Hom.: 167

Bravo AF: 0.318

Asia WGS AF: 0.279 AC: 972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.40
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: rs7443543; hg19: chr5-163872068; COSMIC: COSV72126918;