rs9314033

chr5-164463200-A-Cchr5-164463200-A-Gchr5-164463200-A-T

Variant summary

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

The NR_105064.1(LINC02143):n.120+1599T>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 0.896 in 152,138 control chromosomes in the GnomAD database, including 61,261 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 0.90 (61261 hom., cov: 32)
• Consequence: LINC02143 NR_105064.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

Genes affected

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

LINC02143 (HGNC:53003): (long intergenic non-protein coding RNA 2143)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02143	NR_105064.1	n.120+1599T>G		intron_variant, non_coding_transcript_variant
LINC03000	XR_001742489.2	n.576+108976A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03000	ENST00000519570.5	n.303+108976A>C		intron_variant, non_coding_transcript_variant		3
LINC02143	ENST00000519929.2	n.597+1599T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.895 AC: 136126 AN: 152020 Hom.: 61205 Cov.: 32

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.855

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.901

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

GnomAD4 genome AF: 0.896 AC: 136240 AN: 152138 Hom.: 61261 Cov.: 32 AF XY: 0.894 AC XY: 66503 AN XY: 74364

Gnomad4 AFR AF: 0.945

Gnomad4 AMR AF: 0.917

Gnomad4 ASJ AF: 0.885

Gnomad4 EAS AF: 0.659

Gnomad4 SAS AF: 0.872

Gnomad4 FIN AF: 0.855

Gnomad4 NFE AF: 0.886

Gnomad4 OTH AF: 0.898

Alfa AF: 0.893 Hom.: 4432

Bravo AF: 0.899

Asia WGS AF: 0.788 AC: 2743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.69
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9314033; hg19: chr5-163890206;