rs11123148

Variant names:

• chr2-112732746-G-A
• rs11123148
• NM_001393655.1:c.1344+3042G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
NT5DC4	NM_001393655.1	c.1344+3042G>A		intron_variant	Intron 16 of 16	ENST00000688554.1	NP_001380584.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NT5DC4	ENST00000688554.1	c.1344+3042G>A		intron_variant	Intron 16 of 16		NM_001393655.1	ENSP00000509504.1

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

African (AFR) AF: 0.340 AC: 14076 AN: 41442

American (AMR) AF: 0.324 AC: 4948 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1505 AN: 3468

East Asian (EAS) AF: 0.246 AC: 1270 AN: 5166

South Asian (SAS) AF: 0.457 AC: 2195 AN: 4802

European-Finnish (FIN) AF: 0.421 AC: 4449 AN: 10580

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30200 AN: 67952

Other (OTH) AF: 0.384 AC: 812 AN: 2116

Alfa AF: 0.410 Hom.: 5109

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
PhyloP100		0.27
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11123148; hg19: chr2-113490323;