14-73977387-GAAAA-GAA

Position:

• chr14-73977387-GAAAA-GAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001249.5(ENTPD5):​c.442-15_442-14delTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00411 in 1,137,072 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0016 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0044 (0 hom.)
• Consequence: ENTPD5 NM_001249.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENTPD5	NM_001249.5	c.442-15_442-14delTT		intron_variant		ENST00000334696.11	NP_001240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENTPD5	ENST00000334696.11	c.442-15_442-14delTT		intron_variant		5	NM_001249.5	ENSP00000335246.6
ENTPD5	ENST00000557325.5	c.442-15_442-14delTT		intron_variant		2		ENSP00000451810.1
ENTPD5	ENST00000553284.5	c.442-15_442-14delTT		intron_variant		3		ENSP00000451591.1

Frequencies

GnomAD3 genomes AF: 0.00158 AC: 193 AN: 122278 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00596

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000328

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000151

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000336

Gnomad OTH AF: 0.000606

GnomAD4 exome AF: 0.00441 AC: 4480 AN: 1014772 Hom.: 0 AF XY: 0.00431 AC XY: 2236 AN XY: 518390

Gnomad4 AFR exome AF: 0.0141

Gnomad4 AMR exome AF: 0.00786

Gnomad4 ASJ exome AF: 0.00431

Gnomad4 EAS exome AF: 0.00858

Gnomad4 SAS exome AF: 0.00413

Gnomad4 FIN exome AF: 0.00487

Gnomad4 NFE exome AF: 0.00381

Gnomad4 OTH exome AF: 0.00449

GnomAD4 genome AF: 0.00158 AC: 193 AN: 122300 Hom.: 0 Cov.: 0 AF XY: 0.00159 AC XY: 93 AN XY: 58540

Gnomad4 AFR AF: 0.00595

Gnomad4 AMR AF: 0.000327

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000151

Gnomad4 NFE AF: 0.0000336

Gnomad4 OTH AF: 0.000602

ClinVar

Not reported in ClinVar

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;