chr16-5111773-T-G

Variant names:

• chr16-5111773-T-G
• rs12381130

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 0.817 in 151,650 control chromosomes in the GnomAD database, including 51,151 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 0.82 (51151 hom., cov: 30)
• Consequence: ENPP7P14 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 5 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENPP7P14		n.5111773T>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285567	ENST00000589323.1	n.247+12788T>G		intron_variant	Intron 1 of 3	5
ENPP7P14	ENST00000621765.1	n.403-343A>C		intron_variant	Intron 2 of 2	6
ENSG00000285567	ENST00000650622.1	n.96+4006T>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.817 AC: 123790 AN: 151532 Hom.: 51090 Cov.: 30

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.817 AC: 123906 AN: 151650 Hom.: 51151 Cov.: 30 AF XY: 0.817 AC XY: 60503 AN XY: 74092

African (AFR) AF: 0.938 AC: 38826 AN: 41414

American (AMR) AF: 0.717 AC: 10926 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2679 AN: 3462

East Asian (EAS) AF: 0.755 AC: 3870 AN: 5128

South Asian (SAS) AF: 0.848 AC: 4068 AN: 4796

European-Finnish (FIN) AF: 0.798 AC: 8390 AN: 10508

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.774 AC: 52477 AN: 67816

Other (OTH) AF: 0.812 AC: 1707 AN: 2102

Alfa AF: 0.801 Hom.: 7768

Bravo AF: 0.816

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	7.5
DANN	Benign	0.35
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs12381130; hg19: chr16-5161774;