chr14-73977387-GA-G

Position:

• chr14-73977387-GA-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001249.5(ENTPD5):​c.442-14delT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.015 (40 hom., cov: 0)
  • Exomes 𝑓: 0.12 (3 hom.)
• Consequence: ENTPD5 NM_001249.5 intron
• Clinical Significance: Not reported in ClinVar
• 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 -8 ACMG points.

• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0147 AC: 1791 AN: 122186 Hom.: 39 Cov.: 0

Gnomad AFR AF: 0.0513

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00664

Gnomad ASJ AF: 0.000974

Gnomad EAS AF: 0.00112

Gnomad SAS AF: 0.000547

Gnomad FIN AF: 0.00333

Gnomad MID AF: 0.0115

Gnomad NFE AF: 0.00109

Gnomad OTH AF: 0.0133

GnomAD4 exome AF: 0.119 AC: 117097 AN: 981186 Hom.: 3 Cov.: 14 AF XY: 0.121 AC XY: 60633 AN XY: 499134

Gnomad4 AFR exome AF: 0.236

Gnomad4 AMR exome AF: 0.166

Gnomad4 ASJ exome AF: 0.127

Gnomad4 EAS exome AF: 0.286

Gnomad4 SAS exome AF: 0.178

Gnomad4 FIN exome AF: 0.108

Gnomad4 NFE exome AF: 0.102

Gnomad4 OTH exome AF: 0.131

GnomAD4 genome AF: 0.0147 AC: 1800 AN: 122206 Hom.: 40 Cov.: 0 AF XY: 0.0141 AC XY: 824 AN XY: 58470

Gnomad4 AFR AF: 0.0514

Gnomad4 AMR AF: 0.00663

Gnomad4 ASJ AF: 0.000974

Gnomad4 EAS AF: 0.00141

Gnomad4 SAS AF: 0.000550

Gnomad4 FIN AF: 0.00333

Gnomad4 NFE AF: 0.00109

Gnomad4 OTH AF: 0.0133

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;