14-73977387-GAAAAAA-GAAAAAAA

Variant names:

• chr14-73977387-G-GA
• rs201751093
• NM_001249.5:c.442-14dupT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001249.5(ENTPD5):​c.442-14dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.37 (8564 hom., cov: 0)
  • Exomes 𝑓: 0.32 (2851 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENTPD5 NM_001249.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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: Benign. The variant received -10 ACMG points.

• BP6: Variant 14-73977387-G-GA is Benign according to our data. Variant chr14-73977387-G-GA is described in ClinVar as Benign. ClinVar VariationId is 402829.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

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.442-14dupT		intron	N/A	NP_001240.1	O75356
	ENTPD5	NM_001321985.3		c.442-14dupT		intron	N/A	NP_001308914.1	O75356
	ENTPD5	NM_001321986.3		c.442-14dupT		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_442-13insT		intron	N/A	ENSP00000335246.6	O75356
	ENTPD5	ENST00000900912.1		c.466-14_466-13insT		intron	N/A	ENSP00000570971.1
	ENTPD5	ENST00000900901.1		c.442-14_442-13insT		intron	N/A	ENSP00000570960.1

Frequencies

GnomAD3 genomes AF: 0.373 AC: 45506 AN: 122132 Hom.: 8566 Cov.: 0

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.0618

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.384

GnomAD2 exomes AF: 0.293 AC: 41964 AN: 143370 AF XY: 0.294

Gnomad AFR exome AF: 0.152

Gnomad AMR exome AF: 0.292

Gnomad ASJ exome AF: 0.335

Gnomad EAS exome AF: 0.108

Gnomad FIN exome AF: 0.347

Gnomad NFE exome AF: 0.336

Gnomad OTH exome AF: 0.311

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.319 AC: 322033 AN: 1008174 Hom.: 2851 Cov.: 14 AF XY: 0.317 AC XY: 163290 AN XY: 514430

African (AFR) AF: 0.160 AC: 3549 AN: 22122

American (AMR) AF: 0.267 AC: 8008 AN: 29992

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 6593 AN: 20464

East Asian (EAS) AF: 0.119 AC: 3984 AN: 33394

South Asian (SAS) AF: 0.240 AC: 15869 AN: 66054

European-Finnish (FIN) AF: 0.336 AC: 12997 AN: 38654

Middle Eastern (MID) AF: 0.291 AC: 1263 AN: 4340

European-Non Finnish (NFE) AF: 0.342 AC: 256318 AN: 749530

Other (OTH) AF: 0.308 AC: 13452 AN: 43624

GnomAD4 genome AF: 0.372 AC: 45492 AN: 122154 Hom.: 8564 Cov.: 0 AF XY: 0.371 AC XY: 21702 AN XY: 58456

African (AFR) AF: 0.168 AC: 5213 AN: 31038

American (AMR) AF: 0.402 AC: 4901 AN: 12204

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1390 AN: 3080

East Asian (EAS) AF: 0.0617 AC: 219 AN: 3552

South Asian (SAS) AF: 0.293 AC: 1062 AN: 3630

European-Finnish (FIN) AF: 0.495 AC: 3268 AN: 6596

Middle Eastern (MID) AF: 0.354 AC: 85 AN: 240

European-Non Finnish (NFE) AF: 0.478 AC: 28374 AN: 59370

Other (OTH) AF: 0.384 AC: 637 AN: 1658

Alfa AF: 0.00 Hom.: 0

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.24
Mutation Taster		=100/0	polymorphism (auto)

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; COSMIC: COSV58223510; COSMIC: COSV58223510;