chr5-112644409-T-C

Position:

• chr5-112644409-T-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02200	ENST00000690425.1	n.498+12312T>C		intron_variant, non_coding_transcript_variant

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;