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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000796740.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303727	ENST00000796740.1		n.152+35458T>G		intron	N/A
	ENSG00000303752	ENST00000796976.1		n.701+4491A>C		intron	N/A
	ENSG00000303752	ENST00000796977.1		n.201+4833A>C		intron	N/A

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 v4.9

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;