ENST00000690425.1:n.498+12312T>C

Variant names:

• chr5-112644409-T-C
• rs748628
• ENST00000690425.1:n.498+12312T>C

Variant summary

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

The ENST00000690425.1(LINC02200):​n.498+12312T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 152,082 control chromosomes in the GnomAD database, including 38,698 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 0.71 (38698 hom., cov: 31)
• Consequence: LINC02200 ENST00000690425.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.534

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.766 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	ENST00000690425.1	n.498+12312T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.711 AC: 107992 AN: 151964 Hom.: 38666 Cov.: 31

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.744

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.742

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.711 AC: 108075 AN: 152082 Hom.: 38698 Cov.: 31 AF XY: 0.714 AC XY: 53101 AN XY: 74342

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.784

Gnomad4 EAS AF: 0.720

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.756

Gnomad4 NFE AF: 0.742

Gnomad4 OTH AF: 0.690

Alfa AF: 0.736 Hom.: 58717

Bravo AF: 0.710

Asia WGS AF: 0.720 AC: 2503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.86
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs748628; hg19: chr5-111980106;