NM_173474.4:c.81+1102G>T

Variant names:

• chr16-15054789-C-A
• rs11075253
• NM_173474.4:c.81+1102G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173474.4(NTAN1):​c.81+1102G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,134 control chromosomes in the GnomAD database, including 4,406 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 0.22 (4406 hom., cov: 32)
• Consequence: NTAN1 NM_173474.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240
• Publications: 29 publications found

Genes affected

NTAN1 (HGNC:29909): (N-terminal asparagine amidase) The protein encoded by this gene functions in a step-wise process of protein degradation through the N-end rule pathway. This protein acts as a tertiary destabilizing enzyme that deamidates N-terminal L-Asn residues on proteins to produce N-terminal L-Asp. L-Asp substrates are subsequently conjugated to L-Arg, which is recognized by specific E3 ubiquitin ligases and targeted to the proteasome. Pseudogenes of this gene are located on the long arms of chromosomes 8, 10 and 12. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, Jul 2012]

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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173474.4. 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
	NTAN1	NM_173474.4	MANE Select	c.81+1102G>T		intron	N/A	NP_775745.1
	PDXDC1	NM_001285449.2		c.1399+24733C>A		intron	N/A	NP_001272378.1
	PDXDC1	NM_001324020.2		c.1396+24733C>A		intron	N/A	NP_001310949.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NTAN1	ENST00000287706.8	TSL:1 MANE Select	c.81+1102G>T		intron	N/A	ENSP00000287706.3
	PDXDC1	ENST00000535621.6	TSL:1	c.1399+24733C>A		intron	N/A	ENSP00000437835.2
	PDXDC1	ENST00000850604.1		c.1399+24733C>A		intron	N/A	ENSP00000520891.1

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33546 AN: 152014 Hom.: 4411 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.220 AC: 33530 AN: 152134 Hom.: 4406 Cov.: 32 AF XY: 0.217 AC XY: 16170 AN XY: 74364

African (AFR) AF: 0.107 AC: 4455 AN: 41520

American (AMR) AF: 0.205 AC: 3131 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1220 AN: 3468

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5180

South Asian (SAS) AF: 0.158 AC: 761 AN: 4824

European-Finnish (FIN) AF: 0.274 AC: 2894 AN: 10576

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20040 AN: 67984

Other (OTH) AF: 0.253 AC: 534 AN: 2112

Alfa AF: 0.263 Hom.: 16797

Bravo AF: 0.211

Asia WGS AF: 0.0770 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.3
DANN	Benign	0.80
PhyloP100		-0.024
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: rs11075253; hg19: chr16-15148646;