14-73977387-GAAAAAA-GAAAAAAAAAA

Variant names:

• chr14-73977387-G-GAAAA
• rs201751093
• NM_001249.5:c.442-17_442-14dupTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001249.5(ENTPD5):​c.442-17_442-14dupTTTT 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 0.0 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000016 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENTPD5 NM_001249.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.242
• Publications: 0 publications found

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

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001249.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTPD5	NM_001249.5	MANE Select	c.442-17_442-14dupTTTT		intron	N/A	NP_001240.1	O75356
	ENTPD5	NM_001321985.3		c.442-17_442-14dupTTTT		intron	N/A	NP_001308914.1	O75356
	ENTPD5	NM_001321986.3		c.442-17_442-14dupTTTT		intron	N/A	NP_001308915.1	O75356

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTPD5	ENST00000334696.11	TSL:5 MANE Select	c.442-14_442-13insTTTT		intron	N/A	ENSP00000335246.6	O75356
	ENTPD5	ENST00000900912.1		c.466-14_466-13insTTTT		intron	N/A	ENSP00000570971.1
	ENTPD5	ENST00000900901.1		c.442-14_442-13insTTTT		intron	N/A	ENSP00000570960.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 122294 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000165 AC: 17 AN: 1030576 Hom.: 0 Cov.: 14 AF XY: 0.0000190 AC XY: 10 AN XY: 526616

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 22748

American (AMR) AF: 0.00 AC: 0 AN: 30852

Ashkenazi Jewish (ASJ) AF: 0.0000951 AC: 2 AN: 21020

East Asian (EAS) AF: 0.00 AC: 0 AN: 34824

South Asian (SAS) AF: 0.0000145 AC: 1 AN: 68826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 39630

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4452

European-Non Finnish (NFE) AF: 0.0000183 AC: 14 AN: 763600

Other (OTH) AF: 0.00 AC: 0 AN: 44624

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 122294 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 58512

African (AFR) AF: 0.00 AC: 0 AN: 31020

American (AMR) AF: 0.00 AC: 0 AN: 12210

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3086

East Asian (EAS) AF: 0.00 AC: 0 AN: 3562

South Asian (SAS) AF: 0.00 AC: 0 AN: 3656

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6608

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 262

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 59454

Other (OTH) AF: 0.00 AC: 0 AN: 1650

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs201751093; hg19: chr14-74444090;