rs3176892

Variant names:

• chr10-95755831-T-C
• rs3176892
• ENST00000453258.6:c.37+43838T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-95755831-T-C
• chr10-95755831-T-A

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BS1 BS2

The NM_001164178.1(ENTPD1):​c.52+65T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.042 in 1,511,276 control chromosomes in the GnomAD database, including 1,540 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.034 (119 hom., cov: 31)
  • Exomes 𝑓: 0.043 (1421 hom.)
• Consequence: ENTPD1 NM_001164178.1 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.192
• Publications: 7 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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 10-95755831-T-C is Benign according to our data. Variant chr10-95755831-T-C is described in ClinVar as Benign. ClinVar VariationId is 1234750.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0338 (5131/151994) while in subpopulation NFE AF = 0.0494 (3356/67976). AF 95% confidence interval is 0.048. There are 119 homozygotes in GnomAd4. There are 2470 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 119 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001164178.1. 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_001164178.1		c.52+65T>C		intron	N/A	NP_001157650.1	P49961-6
	ENTPD1	NM_001098175.2		c.37+43838T>C		intron	N/A	NP_001091645.1	P49961-2
	ENTPD1	NM_001440933.1		c.37+43838T>C		intron	N/A	NP_001427862.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTPD1	ENST00000453258.6	TSL:1	c.37+43838T>C		intron	N/A	ENSP00000390955.2	P49961-2
	ENTPD1	ENST00000371207.8	TSL:2	c.52+65T>C		intron	N/A	ENSP00000360250.3	P49961-6
	ENTPD1	ENST00000543964.6	TSL:2	c.-181+65T>C		intron	N/A	ENSP00000442968.1	P49961-5

Frequencies

GnomAD3 genomes AF: 0.0338 AC: 5136 AN: 151876 Hom.: 119 Cov.: 31

Gnomad AFR AF: 0.0148

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0275

Gnomad ASJ AF: 0.0553

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0104

Gnomad FIN AF: 0.0380

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0494

Gnomad OTH AF: 0.0345

GnomAD4 exome AF: 0.0429 AC: 58335 AN: 1359282 Hom.: 1421 Cov.: 25 AF XY: 0.0424 AC XY: 28508 AN XY: 672240

African (AFR) AF: 0.0141 AC: 438 AN: 30968

American (AMR) AF: 0.0224 AC: 799 AN: 35592

Ashkenazi Jewish (ASJ) AF: 0.0578 AC: 1448 AN: 25032

East Asian (EAS) AF: 0.000337 AC: 12 AN: 35602

South Asian (SAS) AF: 0.0138 AC: 1084 AN: 78652

European-Finnish (FIN) AF: 0.0441 AC: 1545 AN: 35054

Middle Eastern (MID) AF: 0.0392 AC: 221 AN: 5640

European-Non Finnish (NFE) AF: 0.0480 AC: 50641 AN: 1055722

Other (OTH) AF: 0.0377 AC: 2147 AN: 57020

GnomAD4 genome AF: 0.0338 AC: 5131 AN: 151994 Hom.: 119 Cov.: 31 AF XY: 0.0332 AC XY: 2470 AN XY: 74288

African (AFR) AF: 0.0148 AC: 612 AN: 41414

American (AMR) AF: 0.0274 AC: 418 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0553 AC: 192 AN: 3470

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5170

South Asian (SAS) AF: 0.00996 AC: 48 AN: 4818

European-Finnish (FIN) AF: 0.0380 AC: 401 AN: 10562

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0494 AC: 3356 AN: 67976

Other (OTH) AF: 0.0342 AC: 72 AN: 2108

Alfa AF: 0.0429 Hom.: 201

Bravo AF: 0.0318

Asia WGS AF: 0.00606 AC: 21 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.8
DANN	Benign	0.70
PhyloP100		0.19
PromoterAI		0.026	Neutral
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs3176892; hg19: chr10-97515588;