NM_001776.6:c.144+3746A>T

Variant names:

• chr10-95827110-A-T
• rs10748648
• NM_001776.6:c.144+3746A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001776.6(ENTPD1):​c.144+3746A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 151,928 control chromosomes in the GnomAD database, including 22,540 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.54 (22540 hom., cov: 31)
• Consequence: ENTPD1 NM_001776.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.756
• Publications: 3 publications found

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]

ENTPD1-AS1 (HGNC:45203): (ENTPD1 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001776.6. 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
	ENTPD1	NM_001776.6	MANE Select	c.144+3746A>T		intron	N/A	NP_001767.3
	ENTPD1	NM_001440932.1		c.222+3746A>T		intron	N/A	NP_001427861.1
	ENTPD1	NM_001164178.1		c.180+3746A>T		intron	N/A	NP_001157650.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTPD1	ENST00000371205.5	TSL:1 MANE Select	c.144+3746A>T		intron	N/A	ENSP00000360248.4
	ENTPD1	ENST00000453258.6	TSL:1	c.165+3746A>T		intron	N/A	ENSP00000390955.2
	ENTPD1	ENST00000635076.1	TSL:1	n.144+3746A>T		intron	N/A	ENSP00000489250.1

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81889 AN: 151810 Hom.: 22517 Cov.: 31

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.504

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.539 AC: 81962 AN: 151928 Hom.: 22540 Cov.: 31 AF XY: 0.542 AC XY: 40240 AN XY: 74250

African (AFR) AF: 0.545 AC: 22548 AN: 41402

American (AMR) AF: 0.629 AC: 9615 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1340 AN: 3470

East Asian (EAS) AF: 0.261 AC: 1350 AN: 5164

South Asian (SAS) AF: 0.563 AC: 2712 AN: 4818

European-Finnish (FIN) AF: 0.557 AC: 5869 AN: 10530

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.541 AC: 36793 AN: 67952

Other (OTH) AF: 0.501 AC: 1059 AN: 2112

Alfa AF: 0.541 Hom.: 2727

Bravo AF: 0.543

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.57
DANN	Benign	0.67
PhyloP100		-0.76
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: rs10748648; hg19: chr10-97586867;