chr5-112680881-T-C

Position:

• chr5-112680881-T-C

Variant summary

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

The NR_104673.1(LOC102467216):​n.45+1963A>G 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 0.169 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: LOC102467216 NR_104673.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

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 (NFE) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102467216	NR_104673.1	n.45+1963A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02200	ENST00000690425.1	n.499-921T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.0562

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.172

Alfa AF: 0.166 Hom.: 1273

Bravo AF: 0.164

Asia WGS AF: 0.119 AC: 412 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	0.50
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13358140; hg19: chr5-112016578;