rs11123148

chr2-112732746-G-A

Variant summary

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

The NM_001393655.1(NT5DC4):c.1344+3042G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 152,008 control chromosomes in the GnomAD database, including 12,042 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 0.39 (12042 hom., cov: 31)
• Consequence: NT5DC4 NM_001393655.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274

Genes affected

NT5DC4 (HGNC:27678): (5'-nucleotidase domain containing 4) Predicted to enable 5'-nucleotidase activity. Predicted to be involved in dephosphorylation. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NT5DC4	NM_001393655.1	c.1344+3042G>A		intron_variant		ENST00000688554.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NT5DC4	ENST00000688554.1	c.1344+3042G>A		intron_variant			NM_001393655.1

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59997 AN: 151888 Hom.: 12048 Cov.: 31

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.395 AC: 59992 AN: 152008 Hom.: 12042 Cov.: 31 AF XY: 0.390 AC XY: 29009 AN XY: 74314

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.434

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.384

Alfa AF: 0.407 Hom.: 3942

Bravo AF: 0.380

Asia WGS AF: 0.350 AC: 1215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	6.5
Dann	Benign	0.85

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11123148; hg19: chr2-113490323;