chr14-73977387-GAAA-G

Variant names:

• chr14-73977387-GAAA-G
• rs201751093
• NM_001249.5:c.442-16_442-14delTTT

Variant summary

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

The ENST00000334696.11(ENTPD5):​c.442-16_442-14delTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000336 in 1,028,306 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 0.0 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00034 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENTPD5 ENST00000334696.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• 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: ENST00000334696.11. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTPD5	NM_001249.5	MANE Select	c.442-16_442-14delTTT		intron	N/A	NP_001240.1
	ENTPD5	NM_001321985.3		c.442-16_442-14delTTT		intron	N/A	NP_001308914.1
	ENTPD5	NM_001321986.3		c.442-16_442-14delTTT		intron	N/A	NP_001308915.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTPD5	ENST00000334696.11	TSL:5 MANE Select	c.442-16_442-14delTTT		intron	N/A	ENSP00000335246.6
	ENTPD5	ENST00000557325.5	TSL:2	c.442-16_442-14delTTT		intron	N/A	ENSP00000451810.1
	ENTPD5	ENST00000553284.5	TSL:3	c.442-16_442-14delTTT		intron	N/A	ENSP00000451591.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 122290 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

GnomAD2 exomes AF: 0.00113 AC: 162 AN: 143370 AF XY: 0.00109

Gnomad AFR exome AF: 0.00351

Gnomad AMR exome AF: 0.000836

Gnomad ASJ exome AF: 0.000980

Gnomad EAS exome AF: 0.00163

Gnomad FIN exome AF: 0.000974

Gnomad NFE exome AF: 0.000896

Gnomad OTH exome AF: 0.00174

GnomAD4 exome AF: 0.000336 AC: 345 AN: 1028306 Hom.: 0 AF XY: 0.000346 AC XY: 182 AN XY: 525474

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

African (AFR) AF: 0.000530 AC: 12 AN: 22652

American (AMR) AF: 0.000520 AC: 16 AN: 30746

Ashkenazi Jewish (ASJ) AF: 0.000334 AC: 7 AN: 20966

East Asian (EAS) AF: 0.000462 AC: 16 AN: 34600

South Asian (SAS) AF: 0.000452 AC: 31 AN: 68620

European-Finnish (FIN) AF: 0.000582 AC: 23 AN: 39526

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4450

European-Non Finnish (NFE) AF: 0.000303 AC: 231 AN: 762230

Other (OTH) AF: 0.000202 AC: 9 AN: 44516

⚠️ 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: 122290 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: 12208

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: 6606

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		1.2
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs201751093; hg19: chr14-74444090;