chr5-112634867-C-G

Variant names:

• chr5-112634867-C-G
• rs964417
• ENST00000653123.1:n.462+2770C>G

Variant summary

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

The ENST00000653123.1(LINC02200):​n.462+2770C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 152,086 control chromosomes in the GnomAD database, including 25,704 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 0.57 (25704 hom., cov: 33)
• Consequence: LINC02200 ENST00000653123.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.337

Genes affected

LINC02200 (HGNC:53066): (long intergenic non-protein coding RNA 2200)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02200	ENST00000653123.1	n.462+2770C>G		intron_variant	Intron 4 of 4
LINC02200	ENST00000663305.1	n.612+2770C>G		intron_variant	Intron 4 of 4
LINC02200	ENST00000690425.1	n.498+2770C>G		intron_variant	Intron 4 of 4
LINC02200	ENST00000667476.1	n.*244C>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86497 AN: 151968 Hom.: 25705 Cov.: 33

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.569 AC: 86517 AN: 152086 Hom.: 25704 Cov.: 33 AF XY: 0.574 AC XY: 42661 AN XY: 74362

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.710

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.573

Alfa AF: 0.588 Hom.: 3238

Bravo AF: 0.559

Asia WGS AF: 0.669 AC: 2323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.6
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs964417; hg19: chr5-111970564;