14-73977387-GAAAA-GAAAAAA

Position:

• chr14-73977387-GAAAA-GAAAAAA

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS1

The NM_001249.5(ENTPD5):​c.442-15_442-14dupTT 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 0.00047 (0 hom., cov: 0)
  • Exomes 𝑓: 0.018 (0 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 Likely_benign. Variant got -4 ACMG points.

• BS1: Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.0178 (18233/1022944) while in subpopulation NFE AF= 0.0205 (15523/757716). AF 95% confidence interval is 0.0202. There are 0 homozygotes in gnomad4_exome. There are 8837 alleles in male gnomad4_exome subpopulation. Median coverage is 14. This position pass quality control queck.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENTPD5	ENST00000334696.11	c.442-14_442-13insTT		intron_variant		5	NM_001249.5	ENSP00000335246.6
ENTPD5	ENST00000557325.5	c.442-14_442-13insTT		intron_variant		2		ENSP00000451810.1
ENTPD5	ENST00000553284.5	c.442-14_442-13insTT		intron_variant		3		ENSP00000451591.1

Frequencies

GnomAD3 genomes AF: 0.000466 AC: 57 AN: 122278 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000226

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000655

Gnomad ASJ AF: 0.00162

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000303

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000555

Gnomad OTH AF: 0.00121

GnomAD4 exome AF: 0.0178 AC: 18233 AN: 1022944 Hom.: 0 Cov.: 14 AF XY: 0.0169 AC XY: 8837 AN XY: 522750

Gnomad4 AFR exome AF: 0.00464

Gnomad4 AMR exome AF: 0.0117

Gnomad4 ASJ exome AF: 0.0161

Gnomad4 EAS exome AF: 0.00187

Gnomad4 SAS exome AF: 0.00803

Gnomad4 FIN exome AF: 0.0144

Gnomad4 NFE exome AF: 0.0205

Gnomad4 OTH exome AF: 0.0155

GnomAD4 genome AF: 0.000466 AC: 57 AN: 122300 Hom.: 0 Cov.: 0 AF XY: 0.000615 AC XY: 36 AN XY: 58536

Gnomad4 AFR AF: 0.000225

Gnomad4 AMR AF: 0.000654

Gnomad4 ASJ AF: 0.00162

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000303

Gnomad4 NFE AF: 0.000555

Gnomad4 OTH AF: 0.00120

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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;