rs1121

Variant names:

• chr16-15037219-G-A
• rs1121
• NM_015027.4:c.*944G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-15037219-G-A
• chr16-15037219-G-T

Variant summary

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

The NM_015027.4(PDXDC1):​c.*944G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 152,046 control chromosomes in the GnomAD database, including 7,446 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 0.30 (7445 hom., cov: 32)
  • Exomes 𝑓: 0.38 (1 hom.)
• Consequence: PDXDC1 NM_015027.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233
• Publications: 27 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDXDC1	NM_015027.4	c.*944G>A		3_prime_UTR_variant	Exon 23 of 23	ENST00000396410.9	NP_055842.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDXDC1	ENST00000396410.9	c.*944G>A		3_prime_UTR_variant	Exon 23 of 23	1	NM_015027.4	ENSP00000379691.4

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45853 AN: 151912 Hom.: 7423 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.315

GnomAD4 exome AF: 0.375 AC: 6 AN: 16 Hom.: 1 Cov.: 0 AF XY: 0.200 AC XY: 2 AN XY: 10

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.357 AC: 5 AN: 14

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.302 AC: 45922 AN: 152030 Hom.: 7445 Cov.: 32 AF XY: 0.308 AC XY: 22866 AN XY: 74306

African (AFR) AF: 0.216 AC: 8934 AN: 41452

American (AMR) AF: 0.440 AC: 6720 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1104 AN: 3472

East Asian (EAS) AF: 0.384 AC: 1982 AN: 5158

South Asian (SAS) AF: 0.403 AC: 1941 AN: 4820

European-Finnish (FIN) AF: 0.339 AC: 3587 AN: 10566

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20681 AN: 67988

Other (OTH) AF: 0.321 AC: 675 AN: 2102

Alfa AF: 0.302 Hom.: 10130

Bravo AF: 0.309

Asia WGS AF: 0.425 AC: 1475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.1
DANN	Benign	0.64
PhyloP100		0.23
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs1121; hg19: chr16-15131076;