NM_001393655.1:c.1344+1974C>G

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001393655.1(NT5DC4):​c.1344+1974C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: NT5DC4 NM_001393655.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290
• Publications: 4 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001393655.1. 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
	NT5DC4	NM_001393655.1	MANE Select	c.1344+1974C>G		intron	N/A	NP_001380584.1	Q86YG4-2
	NT5DC4	NM_001350494.2		c.1248+1974C>G		intron	N/A	NP_001337423.1	Q86YG4-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NT5DC4	ENST00000688554.1	MANE Select	c.1344+1974C>G		intron	N/A	ENSP00000509504.1	Q86YG4-2
	NT5DC4	ENST00000327581.4	TSL:1	c.1248+1974C>G		intron	N/A	ENSP00000330247.4	Q86YG4-1
	NT5DC4	ENST00000690591.1		c.1344+1974C>G		intron	N/A	ENSP00000508583.1	A0A8I5KQQ4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	1.2
DANN	Benign	0.85
PhyloP100		-0.029

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: rs12622683; hg19: chr2-113489255;