rs11718621

Variant names:

• chr3-40320631-T-C
• rs11718621
• ENST00000439293.5:n.144-6434A>G

Variant summary

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

The ENST00000439293.5(ENTPD3-AS1):​n.144-6434A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152
• Publications: 9 publications found

Genes affected

ENTPD3-AS1 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439293.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTPD3-AS1	ENST00000439293.5	TSL:4	n.144-6434A>G		intron	N/A
	ENTPD3-AS1	ENST00000715680.1		n.307-19235A>G		intron	N/A
	ENTPD3-AS1	ENST00000782695.1		n.397+5519A>G		intron	N/A

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

African (AFR) AF: 0.197 AC: 8174 AN: 41520

American (AMR) AF: 0.523 AC: 7987 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1775 AN: 3470

East Asian (EAS) AF: 0.241 AC: 1250 AN: 5178

South Asian (SAS) AF: 0.383 AC: 1850 AN: 4824

European-Finnish (FIN) AF: 0.590 AC: 6229 AN: 10560

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41839 AN: 67990

Other (OTH) AF: 0.477 AC: 1006 AN: 2110

Alfa AF: 0.562 Hom.: 45747

Bravo AF: 0.449

Asia WGS AF: 0.313 AC: 1089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.0
DANN	Benign	0.82
PhyloP100		0.15

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11718621;

hg19: chr3-40362122;