2-112731678-C-T

Variant names:

• chr2-112731678-C-T
• rs12622683
• NM_001393655.1:c.1344+1974C>T

Variant summary

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

The NM_001393655.1(NT5DC4):​c.1344+1974C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 152,020 control chromosomes in the GnomAD database, including 18,595 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 0.49 (18594 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: NT5DC4 NM_001393655.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290

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=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NT5DC4	NM_001393655.1	c.1344+1974C>T		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+1974C>T		intron_variant	Intron 16 of 16		NM_001393655.1	ENSP00000509504.1

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74660 AN: 151898 Hom.: 18565 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.496

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 FIN exome AF: 1.00

GnomAD4 genome AF: 0.492 AC: 74736 AN: 152018 Hom.: 18594 Cov.: 32 AF XY: 0.496 AC XY: 36815 AN XY: 74298

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.501

Alfa AF: 0.499 Hom.: 31495

Bravo AF: 0.492

Asia WGS AF: 0.576 AC: 2006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	1.8
DANN	Benign	0.82

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: rs12622683; hg19: chr2-113489255;