14-80169504-G-C

Variant names:

• chr14-80169504-G-C
• rs54566
• XR_944072.2:n.342-1412C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_944072.2(LOC105370593):​n.342-1412C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 151,978 control chromosomes in the GnomAD database, including 2,541 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 0.16 (2541 hom., cov: 32)
• Consequence: LOC105370593 XR_944072.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240
• Publications: 5 publications found

Genes affected

LOC105370593 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24363 AN: 151860 Hom.: 2537 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.0877

Gnomad ASJ AF: 0.0987

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.160 AC: 24382 AN: 151978 Hom.: 2541 Cov.: 32 AF XY: 0.160 AC XY: 11874 AN XY: 74262

African (AFR) AF: 0.274 AC: 11368 AN: 41430

American (AMR) AF: 0.0876 AC: 1338 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0987 AC: 342 AN: 3466

East Asian (EAS) AF: 0.356 AC: 1831 AN: 5140

South Asian (SAS) AF: 0.108 AC: 520 AN: 4814

European-Finnish (FIN) AF: 0.133 AC: 1410 AN: 10568

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7157 AN: 67974

Other (OTH) AF: 0.144 AC: 304 AN: 2110

Alfa AF: 0.0374 Hom.: 36

Bravo AF: 0.165

Asia WGS AF: 0.240 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.68
DANN	Benign	0.45
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs54566; hg19: chr14-80635847;