16-5111773-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000589323.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000285567	ENST00000589323.1	TSL:5	n.247+12788T>G		intron	N/A
	ENPP7P14	ENST00000621765.1	TSL:6	n.403-343A>C		intron	N/A
	ENSG00000285567	ENST00000650622.1		n.96+4006T>G		intron	N/A

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 v4.9

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;