chr10-95755831-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NR_038444.1(ENTPD1-AS1):​n.1637A>G variant causes a non coding transcript exon 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-AS1
NR_038444.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.192
Variant links:
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)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id 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 male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 119 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ENTPD1-AS1NR_038444.1 linkuse as main transcriptn.1637A>G non_coding_transcript_exon_variant 6/6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENTPD1-AS1ENST00000669711.1 linkuse as main transcriptn.882A>G non_coding_transcript_exon_variant 6/7

Frequencies

GnomAD3 genomes
AF:
0.0338
AC:
5136
AN:
151876
Hom.:
119
Cov.:
31
show subpopulations
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
show subpopulations
Gnomad4 AFR exome
AF:
0.0141
Gnomad4 AMR exome
AF:
0.0224
Gnomad4 ASJ exome
AF:
0.0578
Gnomad4 EAS exome
AF:
0.000337
Gnomad4 SAS exome
AF:
0.0138
Gnomad4 FIN exome
AF:
0.0441
Gnomad4 NFE exome
AF:
0.0480
Gnomad4 OTH exome
AF:
0.0377
GnomAD4 genome
AF:
0.0338
AC:
5131
AN:
151994
Hom.:
119
Cov.:
31
AF XY:
0.0332
AC XY:
2470
AN XY:
74288
show subpopulations
Gnomad4 AFR
AF:
0.0148
Gnomad4 AMR
AF:
0.0274
Gnomad4 ASJ
AF:
0.0553
Gnomad4 EAS
AF:
0.000387
Gnomad4 SAS
AF:
0.00996
Gnomad4 FIN
AF:
0.0380
Gnomad4 NFE
AF:
0.0494
Gnomad4 OTH
AF:
0.0342
Alfa
AF:
0.0448
Hom.:
167
Bravo
AF:
0.0318
Asia WGS
AF:
0.00606
AC:
21
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxApr 08, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
8.8
DANN
Benign
0.70

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3176892; hg19: chr10-97515588; API