chr5-112680881-T-C

Variant names:

• chr5-112680881-T-C
• rs13358140
• ENST00000690425.2:n.723-921T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000690425.2(LINC02200):​n.723-921T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,112 control chromosomes in the GnomAD database, including 2,272 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 0.17 (2272 hom., cov: 32)
• Consequence: LINC02200 ENST00000690425.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 4 publications found

Genes affected

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

ENSG00000300650 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000690425.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC102467216	NR_104673.1		n.45+1963A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02200	ENST00000690425.2		n.723-921T>C		intron	N/A
	ENSG00000300650	ENST00000773182.1		n.137+1963A>G		intron	N/A
	ENSG00000300650	ENST00000773183.1		n.141+1963A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25701 AN: 151994 Hom.: 2273 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.0561

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.169 AC: 25710 AN: 152112 Hom.: 2272 Cov.: 32 AF XY: 0.167 AC XY: 12430 AN XY: 74370

African (AFR) AF: 0.166 AC: 6883 AN: 41500

American (AMR) AF: 0.130 AC: 1983 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 709 AN: 3470

East Asian (EAS) AF: 0.0562 AC: 291 AN: 5174

South Asian (SAS) AF: 0.140 AC: 675 AN: 4818

European-Finnish (FIN) AF: 0.178 AC: 1886 AN: 10580

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12728 AN: 67968

Other (OTH) AF: 0.172 AC: 363 AN: 2114

Alfa AF: 0.167 Hom.: 1410

Bravo AF: 0.164

Asia WGS AF: 0.119 AC: 412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.50
DANN	Benign	0.40
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs13358140; hg19: chr5-112016578;