chr10-95845184-T-C

Variant names:

• chr10-95845184-T-C
• rs3176883
• NM_001776.6:c.574-173T>C

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001776.6(ENTPD1):​c.574-173T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,200 control chromosomes in the GnomAD database, including 2,294 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.15 (2294 hom., cov: 32)
• Consequence: ENTPD1 NM_001776.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0570
• Publications: 2 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)

ENSG00000240527 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 10-95845184-T-C is Benign according to our data. Variant chr10-95845184-T-C is described in ClinVar as Benign. ClinVar VariationId is 1234347.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.259 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTPD1	NM_001776.6	MANE Select	c.574-173T>C		intron	N/A	NP_001767.3
	ENTPD1	NM_001440932.1		c.652-173T>C		intron	N/A	NP_001427861.1
	ENTPD1	NM_001164178.1		c.610-173T>C		intron	N/A	NP_001157650.1	P49961-6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTPD1	ENST00000371205.5	TSL:1 MANE Select	c.574-173T>C		intron	N/A	ENSP00000360248.4	P49961-1
	ENTPD1	ENST00000453258.6	TSL:1	c.595-173T>C		intron	N/A	ENSP00000390955.2	P49961-2
	ENTPD1	ENST00000635076.1	TSL:1	n.*149-173T>C		intron	N/A	ENSP00000489250.1	A0A0U1RQZ5

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23427 AN: 152082 Hom.: 2286 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0891

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0887

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.154 AC: 23486 AN: 152200 Hom.: 2294 Cov.: 32 AF XY: 0.158 AC XY: 11787 AN XY: 74418

African (AFR) AF: 0.263 AC: 10920 AN: 41500

American (AMR) AF: 0.151 AC: 2315 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0891 AC: 309 AN: 3468

East Asian (EAS) AF: 0.175 AC: 903 AN: 5172

South Asian (SAS) AF: 0.245 AC: 1179 AN: 4818

European-Finnish (FIN) AF: 0.135 AC: 1428 AN: 10602

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0887 AC: 6034 AN: 68024

Other (OTH) AF: 0.152 AC: 322 AN: 2112

Alfa AF: 0.0837 Hom.: 189

Bravo AF: 0.157

Asia WGS AF: 0.235 AC: 817 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

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

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.2
DANN	Benign	0.54
PhyloP100		-0.057
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: rs3176883; hg19: chr10-97604941; COSMIC: COSV64603927; COSMIC: COSV64603927;