rs8023192

chr14-20727312-A-Cchr14-20727312-A-G

Variant summary

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

The XR_001750624.2(LOC107984671):n.1442T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 152,072 control chromosomes in the GnomAD database, including 23,181 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 0.55 (23181 hom., cov: 33)
• Consequence: LOC107984671 XR_001750624.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300

Genes affected

LOC107984671 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984671	XR_001750624.2	n.1442T>G		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83572 AN: 151954 Hom.: 23156 Cov.: 33

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.550 AC: 83640 AN: 152072 Hom.: 23181 Cov.: 33 AF XY: 0.554 AC XY: 41198 AN XY: 74332

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.664

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.546

Gnomad4 OTH AF: 0.550

Alfa AF: 0.547 Hom.: 45017

Bravo AF: 0.531

Asia WGS AF: 0.662 AC: 2302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8023192; hg19: chr14-21195471;