ENST00000458228.6:n.298+5675T>C

Variant names:

• chr10-96083591-A-G
• rs7084542
• ENST00000458228.6:n.298+5675T>C

Variant summary

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

The ENST00000458228.6(ENTPD1-AS1):​n.298+5675T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 152,108 control chromosomes in the GnomAD database, including 40,216 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 0.72 (40216 hom., cov: 32)
• Consequence: ENTPD1-AS1 ENST00000458228.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457
• Publications: 2 publications found

Genes affected

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000458228.6. 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-AS1	NR_038444.1		n.296+5675T>C		intron	N/A
	ENTPD1-AS1	NR_134320.1		n.296+5675T>C		intron	N/A
	ENTPD1-AS1	NR_134321.1		n.296+5675T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTPD1-AS1	ENST00000458228.6	TSL:1	n.298+5675T>C		intron	N/A
	ENTPD1-AS1	ENST00000416301.5	TSL:2	n.275+5675T>C		intron	N/A
	ENTPD1-AS1	ENST00000427846.2	TSL:2	n.338+5675T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109389 AN: 151988 Hom.: 40165 Cov.: 32

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.863

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.809

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.720 AC: 109502 AN: 152108 Hom.: 40216 Cov.: 32 AF XY: 0.713 AC XY: 53003 AN XY: 74342

African (AFR) AF: 0.863 AC: 35801 AN: 41488

American (AMR) AF: 0.695 AC: 10614 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.863 AC: 2994 AN: 3470

East Asian (EAS) AF: 0.825 AC: 4273 AN: 5178

South Asian (SAS) AF: 0.657 AC: 3163 AN: 4814

European-Finnish (FIN) AF: 0.553 AC: 5838 AN: 10562

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.653 AC: 44427 AN: 67994

Other (OTH) AF: 0.743 AC: 1571 AN: 2114

Alfa AF: 0.684 Hom.: 11622

Bravo AF: 0.738

Asia WGS AF: 0.764 AC: 2657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.32
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs7084542; hg19: chr10-97843348;