10-96083591-A-G

Position:

• chr10-96083591-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_038444.1(ENTPD1-AS1):​n.296+5675T>C variant causes a intron, non coding transcript 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 NR_038444.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457

Genes affected

ENTPD1-AS1 (HGNC:45203): (ENTPD1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENTPD1-AS1	NR_038444.1	n.296+5675T>C		intron_variant, non_coding_transcript_variant
ENTPD1-AS1	NR_134320.1	n.296+5675T>C		intron_variant, non_coding_transcript_variant
ENTPD1-AS1	NR_134321.1	n.296+5675T>C		intron_variant, non_coding_transcript_variant
ENTPD1-AS1	NR_134322.1	n.296+5675T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENTPD1-AS1	ENST00000669711.1	n.300+5675T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.863

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.863

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.657

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.743

Alfa AF: 0.681 Hom.: 11339

Bravo AF: 0.738

Asia WGS AF: 0.764 AC: 2657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7084542; hg19: chr10-97843348;