rs10428710

Variant names:

• chr5-112671554-C-T
• rs10428710
• ENST00000690425.2:n.723-10248C>T

Variant summary

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

The ENST00000690425.2(LINC02200):​n.723-10248C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 151,948 control chromosomes in the GnomAD database, including 7,095 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 0.28 (7095 hom., cov: 30)
• Consequence: LINC02200 ENST00000690425.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102467216	NR_104673.1	n.45+11290G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02200	ENST00000690425.2	n.723-10248C>T		intron_variant	Intron 4 of 4
ENSG00000300650	ENST00000773182.1	n.137+11290G>A		intron_variant	Intron 1 of 2
ENSG00000300650	ENST00000773183.1	n.141+11290G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42331 AN: 151830 Hom.: 7090 Cov.: 30

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.279 AC: 42352 AN: 151948 Hom.: 7095 Cov.: 30 AF XY: 0.283 AC XY: 20988 AN XY: 74264

African (AFR) AF: 0.131 AC: 5412 AN: 41454

American (AMR) AF: 0.445 AC: 6783 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 912 AN: 3468

East Asian (EAS) AF: 0.615 AC: 3161 AN: 5136

South Asian (SAS) AF: 0.426 AC: 2045 AN: 4804

European-Finnish (FIN) AF: 0.229 AC: 2418 AN: 10564

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20546 AN: 67956

Other (OTH) AF: 0.307 AC: 645 AN: 2102

Alfa AF: 0.298 Hom.: 3700

Bravo AF: 0.292

Asia WGS AF: 0.475 AC: 1650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.62
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs10428710; hg19: chr5-112007251;