rs11718621

chr3-40320631-T-C

Variant summary

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

The ENST00000439293.5(ENTPD3-AS1):n.144-6434A>G 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 0.465 in 152,120 control chromosomes in the GnomAD database, including 19,000 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 0.47 (19000 hom., cov: 32)
• Consequence: ENTPD3-AS1 ENST00000439293.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152

Genes affected

ENTPD3-AS1 (HGNC:26710): (ENTPD3 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ENTPD3-AS1	ENST00000439293.5	n.144-6434A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70720 AN: 152002 Hom.: 18996 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.465 AC: 70745 AN: 152120 Hom.: 19000 Cov.: 32 AF XY: 0.462 AC XY: 34382 AN XY: 74348

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.477

Alfa AF: 0.580 Hom.: 34410

Bravo AF: 0.449

Asia WGS AF: 0.313 AC: 1089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	6.0
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11718621; hg19: chr3-40362122;