16-5111773-T-G

Position:

• chr16-5111773-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000589323.1(ENSG00000267070):​n.247+12788T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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: ENST00000589323.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203

Genes affected

(HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000589323.1	n.247+12788T>G		intron_variant, non_coding_transcript_variant		5
ENPP7P14	ENST00000621765.1	n.403-343A>C		intron_variant, non_coding_transcript_variant
	ENST00000650622.1	n.96+4006T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.938

Gnomad4 AMR AF: 0.717

Gnomad4 ASJ AF: 0.774

Gnomad4 EAS AF: 0.755

Gnomad4 SAS AF: 0.848

Gnomad4 FIN AF: 0.798

Gnomad4 NFE AF: 0.774

Gnomad4 OTH AF: 0.812

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12381130; hg19: chr16-5161774;