10-95711826-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BS1 BS2

The ENST00000453258.6(ENTPD1):c.-131T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0133 in 1,320,992 control chromosomes in the GnomAD database, including 179 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.011 (18 hom., cov: 32)
  • Exomes 𝑓: 0.014 (161 hom.)
• Consequence: ENTPD1 ENST00000453258.6 5_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.238

Genes affected

ENTPD1 (HGNC:3363): (ectonucleoside triphosphate diphosphohydrolase 1) The protein encoded by this gene is a plasma membrane protein that hydrolyzes extracellular ATP and ADP to AMP. Inhibition of this protein's activity may confer anticancer benefits. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2015]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BP6: Variant 10-95711826-T-C is Benign according to our data. Variant chr10-95711826-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1300977.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0114 (1735/152328) while in subpopulation NFE AF= 0.0136 (926/68024). AF 95% confidence interval is 0.0129. There are 18 homozygotes in gnomad4. There are 949 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 18 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ENTPD1	NM_001098175.2	c.-131T>C		5_prime_UTR_variant	1/10
ENTPD1	XM_011540371.3	c.-108-23T>C		intron_variant
ENTPD1	XM_047426023.1	c.-108-23T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ENTPD1	ENST00000453258.6	c.-131T>C		5_prime_UTR_variant	1/10	1

Frequencies

GnomAD3 genomes AF: 0.0114 AC: 1734 AN: 152210 Hom.: 18 Cov.: 32

Gnomad AFR AF: 0.00227

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.00838

Gnomad ASJ AF: 0.00864

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0124

Gnomad FIN AF: 0.0417

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0136

Gnomad OTH AF: 0.0119

GnomAD4 exome AF: 0.0135 AC: 15798 AN: 1168664 Hom.: 161 Cov.: 15 AF XY: 0.0133 AC XY: 7877 AN XY: 594176

Gnomad4 AFR exome AF: 0.00184

Gnomad4 AMR exome AF: 0.00619

Gnomad4 ASJ exome AF: 0.00614

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00775

Gnomad4 FIN exome AF: 0.0386

Gnomad4 NFE exome AF: 0.0143

Gnomad4 OTH exome AF: 0.0106

GnomAD4 genome AF: 0.0114 AC: 1735 AN: 152328 Hom.: 18 Cov.: 32 AF XY: 0.0127 AC XY: 949 AN XY: 74484

Gnomad4 AFR AF: 0.00226

Gnomad4 AMR AF: 0.00836

Gnomad4 ASJ AF: 0.00864

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0124

Gnomad4 FIN AF: 0.0417

Gnomad4 NFE AF: 0.0136

Gnomad4 OTH AF: 0.0118

Alfa AF: 0.0114 Hom.: 2

Bravo AF: 0.00858

Asia WGS AF: 0.00289 AC: 10 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Apr 09, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	4.8
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs146837925; hg19: chr10-97471583;