16-5147394-T-C

Variant names:

• chr16-5147394-T-C
• rs4545817

Variant summary

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

The variant allele was found at a frequency of 0.788 in 151,736 control chromosomes in the GnomAD database, including 48,160 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 0.79 (48160 hom., cov: 34)
• Consequence: ENPP7P14 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.199
• Publications: 1 publications found

Genes affected

ENPP7P14 (HGNC:51387): (ectonucleotide pyrophosphatase/phosphodiesterase 7 pseudogene 14)

ENSG00000285567 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENPP7P14		n.5147394T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENPP7P14	ENST00000621765.1	n.252+1040A>G		intron_variant	Intron 1 of 2	6
ENSG00000285567	ENST00000650622.1	n.96+39627T>C		intron_variant	Intron 1 of 3
ENSG00000285567	ENST00000660079.1	n.119+39544T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.788 AC: 119515 AN: 151622 Hom.: 48144 Cov.: 34

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.918

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.877

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.788 AC: 119580 AN: 151736 Hom.: 48160 Cov.: 34 AF XY: 0.790 AC XY: 58638 AN XY: 74188

African (AFR) AF: 0.610 AC: 25124 AN: 41192

American (AMR) AF: 0.744 AC: 11312 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2818 AN: 3470

East Asian (EAS) AF: 0.793 AC: 4096 AN: 5166

South Asian (SAS) AF: 0.865 AC: 4173 AN: 4826

European-Finnish (FIN) AF: 0.918 AC: 9741 AN: 10610

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.877 AC: 59609 AN: 67968

Other (OTH) AF: 0.805 AC: 1694 AN: 2104

Alfa AF: 0.832 Hom.: 6648

Bravo AF: 0.764

Asia WGS AF: 0.829 AC: 2881 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	5.7
DANN	Benign	0.73
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs4545817; hg19: chr16-5197395;