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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370593	XR_944072.2	n.342-1412C>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;