rs3814159

Variant names:

• chr10-95755380-G-A
• rs3814159
• ENST00000453258.6:c.37+43387G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-95755380-G-A
• chr10-95755380-G-C

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001098175.2(ENTPD1):​c.37+43387G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 270,644 control chromosomes in the GnomAD database, including 33,843 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.50 (19666 hom., cov: 33)
  • Exomes 𝑓: 0.48 (14177 hom.)
• Consequence: ENTPD1 NM_001098175.2 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 0.115
• Publications: 6 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=-0.73).
• BP6: Variant 10-95755380-G-A is Benign according to our data. Variant chr10-95755380-G-A is described in ClinVar as Benign. ClinVar VariationId is 1249702.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001098175.2. 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_001098175.2		c.37+43387G>A		intron	N/A	NP_001091645.1	P49961-2
	ENTPD1	NM_001440933.1		c.37+43387G>A		intron	N/A	NP_001427862.1
	ENTPD1	NM_001440934.1		c.37+43387G>A		intron	N/A	NP_001427863.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTPD1	ENST00000453258.6	TSL:1	c.37+43387G>A		intron	N/A	ENSP00000390955.2	P49961-2
	ENTPD1-AS1	ENST00000416301.5	TSL:2	n.2067C>T		non_coding_transcript_exon	Exon 6 of 6
	ENTPD1-AS1	ENST00000669711.1		n.1333C>T		non_coding_transcript_exon	Exon 6 of 7

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76297 AN: 151988 Hom.: 19651 Cov.: 33

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.466

GnomAD4 exome AF: 0.477 AC: 56569 AN: 118538 Hom.: 14177 Cov.: 0 AF XY: 0.477 AC XY: 29386 AN XY: 61646

African (AFR) AF: 0.506 AC: 2070 AN: 4088

American (AMR) AF: 0.616 AC: 3132 AN: 5082

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1330 AN: 4072

East Asian (EAS) AF: 0.302 AC: 2416 AN: 8004

South Asian (SAS) AF: 0.511 AC: 4569 AN: 8936

European-Finnish (FIN) AF: 0.493 AC: 2905 AN: 5894

Middle Eastern (MID) AF: 0.407 AC: 205 AN: 504

European-Non Finnish (NFE) AF: 0.487 AC: 36359 AN: 74598

Other (OTH) AF: 0.487 AC: 3583 AN: 7360

GnomAD4 genome AF: 0.502 AC: 76361 AN: 152106 Hom.: 19666 Cov.: 33 AF XY: 0.505 AC XY: 37530 AN XY: 74372

African (AFR) AF: 0.518 AC: 21475 AN: 41468

American (AMR) AF: 0.598 AC: 9142 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1149 AN: 3468

East Asian (EAS) AF: 0.261 AC: 1355 AN: 5184

South Asian (SAS) AF: 0.553 AC: 2669 AN: 4826

European-Finnish (FIN) AF: 0.519 AC: 5487 AN: 10574

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33459 AN: 67972

Other (OTH) AF: 0.464 AC: 978 AN: 2110

Alfa AF: 0.492 Hom.: 18978

Bravo AF: 0.507

Asia WGS AF: 0.432 AC: 1504 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)
-	-	1	Hereditary spastic paraplegia 64 (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	9.9
DANN	Benign	0.77
PhyloP100		0.12
PromoterAI		0.0010	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs3814159; hg19: chr10-97515137;