NM_015027.4:c.2107+49A>T

Variant names:

• chr16-15035602-A-T
• rs4985155
• NM_015027.4:c.2107+49A>T

Variant summary

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

The NM_015027.4(PDXDC1):​c.2107+49A>T 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)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PDXDC1 NM_015027.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• Publications: 0 publications found

Genes affected

PDXDC1 (HGNC:28995): (pyridoxal dependent decarboxylase domain containing 1) Enables cadherin binding activity. Predicted to be involved in carboxylic acid metabolic process. Located in Golgi apparatus. [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=-0.79).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015027.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDXDC1	NM_015027.4	MANE Select	c.2107+49A>T		intron	N/A	NP_055842.2
	PDXDC1	NM_001324019.2		c.2104+49A>T		intron	N/A	NP_001310948.1
	PDXDC1	NM_001285447.1		c.2062+49A>T		intron	N/A	NP_001272376.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDXDC1	ENST00000396410.9	TSL:1 MANE Select	c.2107+49A>T		intron	N/A	ENSP00000379691.4
	PDXDC1	ENST00000569715.5	TSL:1	c.2026+49A>T		intron	N/A	ENSP00000455070.1
	PDXDC1	ENST00000535621.6	TSL:1	c.1399+5546A>T		intron	N/A	ENSP00000437835.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 959120 Hom.: 0 Cov.: 12 AF XY: 0.00 AC XY: 0 AN XY: 486698

African (AFR) AF: 0.00 AC: 0 AN: 21962

American (AMR) AF: 0.00 AC: 0 AN: 25108

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19590

East Asian (EAS) AF: 0.00 AC: 0 AN: 33806

South Asian (SAS) AF: 0.00 AC: 0 AN: 64904

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 48738

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3470

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 698542

Other (OTH) AF: 0.00 AC: 0 AN: 43000

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.1
DANN	Benign	0.87
PhyloP100		-0.049
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs4985155; hg19: chr16-15129459;