14-73977387-GAAAA-GAAAAA

Position:

• chr14-73977387-GAAAA-GAAAAA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001249.5(ENTPD5):​c.442-14dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.37 (8564 hom., cov: 0)
  • Exomes 𝑓: 0.32 (2851 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENTPD5 NM_001249.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.242

Genes affected

ENTPD5 (HGNC:3367): (ectonucleoside triphosphate diphosphohydrolase 5 (inactive)) The protein encoded by this gene is similar to E-type nucleotidases (NTPases)/ecto-ATPase/apyrases. NTPases, such as CD39, mediate catabolism of extracellular nucleotides. ENTPD5 contains 4 apyrase-conserved regions which is characteristic of NTPases. [provided by RefSeq, Jan 2009]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 14-73977387-G-GA is Benign according to our data. Variant chr14-73977387-G-GA is described in ClinVar as [Benign]. Clinvar id is 402829.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENTPD5	NM_001249.5	c.442-14dupT		intron_variant		ENST00000334696.11	NP_001240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENTPD5	ENST00000334696.11	c.442-14dupT		intron_variant		5	NM_001249.5	ENSP00000335246.6
ENTPD5	ENST00000557325.5	c.442-14dupT		intron_variant		2		ENSP00000451810.1
ENTPD5	ENST00000553284.5	c.442-14dupT		intron_variant		3		ENSP00000451591.1

Frequencies

GnomAD3 genomes AF: 0.373 AC: 45506 AN: 122132 Hom.: 8566 Cov.: 0

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.0618

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.384

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.319 AC: 322033 AN: 1008174 Hom.: 2851 Cov.: 14 AF XY: 0.317 AC XY: 163290 AN XY: 514430

Gnomad4 AFR exome AF: 0.160

Gnomad4 AMR exome AF: 0.267

Gnomad4 ASJ exome AF: 0.322

Gnomad4 EAS exome AF: 0.119

Gnomad4 SAS exome AF: 0.240

Gnomad4 FIN exome AF: 0.336

Gnomad4 NFE exome AF: 0.342

Gnomad4 OTH exome AF: 0.308

GnomAD4 genome AF: 0.372 AC: 45492 AN: 122154 Hom.: 8564 Cov.: 0 AF XY: 0.371 AC XY: 21702 AN XY: 58456

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.0617

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.384

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs201751093; hg19: chr14-74444090;