rs10428710

chr5-112671554-C-T

Variant summary

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

The NR_104673.1(LOC102467216):n.45+11290G>A 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 0.279 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: LOC102467216 NR_104673.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230

Genes affected

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

LOC102467216 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC102467216	NR_104673.1	n.45+11290G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02200	ENST00000690425.1	n.499-10248C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.615

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.307

Alfa AF: 0.298 Hom.: 3338

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10428710; hg19: chr5-112007251;