14-20727312-A-C

Variant names:

• chr14-20727312-A-C
• rs8023192
• XR_001750624.2:n.1442T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

Genes affected

LOC107984671 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC107984671	XR_001750624.2	n.1442T>G		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303727	ENST00000796740.1	n.152+35458T>G		intron_variant	Intron 2 of 2
ENSG00000303752	ENST00000796976.1	n.701+4491A>C		intron_variant	Intron 1 of 3
ENSG00000303752	ENST00000796977.1	n.201+4833A>C		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.564 AC: 23382 AN: 41478

American (AMR) AF: 0.416 AC: 6356 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1955 AN: 3472

East Asian (EAS) AF: 0.664 AC: 3434 AN: 5172

South Asian (SAS) AF: 0.640 AC: 3087 AN: 4822

European-Finnish (FIN) AF: 0.623 AC: 6591 AN: 10576

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.546 AC: 37099 AN: 67964

Other (OTH) AF: 0.550 AC: 1162 AN: 2112

Alfa AF: 0.544 Hom.: 70909

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
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs8023192; hg19: chr14-21195471;