5-16434781-G-C

Position:

• chr5-16434781-G-C

Variant summary

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

The NR_104625.1(LINC02150):​n.976+2593C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.831 in 151,610 control chromosomes in the GnomAD database, including 52,885 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 0.83 (52885 hom., cov: 27)
• Consequence: LINC02150 NR_104625.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.731

Genes affected

LINC02150 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02150	NR_104625.1	n.976+2593C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02150	ENST00000513157.1	n.961+2593C>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.831 AC: 125857 AN: 151492 Hom.: 52820 Cov.: 27

Gnomad AFR AF: 0.959

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.777

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.831 AC: 125988 AN: 151610 Hom.: 52885 Cov.: 27 AF XY: 0.829 AC XY: 61388 AN XY: 74008

Gnomad4 AFR AF: 0.959

Gnomad4 AMR AF: 0.799

Gnomad4 ASJ AF: 0.790

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.816

Gnomad4 NFE AF: 0.785

Gnomad4 OTH AF: 0.826

Alfa AF: 0.754 Hom.: 2272

Bravo AF: 0.837

Asia WGS AF: 0.747 AC: 2597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.61
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs163065; hg19: chr5-16434890;