5-164445062-T-G

Variant names:

• chr5-164445062-T-G
• rs7443543
• ENST00000486913.3:n.86-41607T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000486913.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03000	ENST00000486913.3	TSL:2	n.86-41607T>G		intron	N/A
	LINC03000	ENST00000517508.5	TSL:4	n.586-41607T>G		intron	N/A
	LINC03000	ENST00000519329.3	TSL:3	n.933-41612T>G		intron	N/A

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

African (AFR) AF: 0.413 AC: 17143 AN: 41480

American (AMR) AF: 0.374 AC: 5709 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1236 AN: 3466

East Asian (EAS) AF: 0.202 AC: 1043 AN: 5168

South Asian (SAS) AF: 0.266 AC: 1283 AN: 4816

European-Finnish (FIN) AF: 0.238 AC: 2519 AN: 10574

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15680 AN: 67962

Other (OTH) AF: 0.318 AC: 672 AN: 2110

Alfa AF: 0.133 Hom.: 213

Bravo AF: 0.318

Asia WGS AF: 0.279 AC: 972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.40
DANN	Benign	0.26
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs7443543; hg19: chr5-163872068; COSMIC: COSV72126918;