chr1-97613672-T-C

Variant names:

• chr1-97613672-T-C
• rs7533902
• NM_000110.4:c.851-18506A>G

Variant summary

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

The NM_000110.4(DPYD):​c.851-18506A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 151,844 control chromosomes in the GnomAD database, including 38,586 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 0.70 (38586 hom., cov: 32)
• Consequence: DPYD NM_000110.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.251
• Publications: 2 publications found

Genes affected

DPYD (HGNC:3012): (dihydropyrimidine dehydrogenase) The protein encoded by this gene is a pyrimidine catabolic enzyme and the initial and rate-limiting factor in the pathway of uracil and thymidine catabolism. Mutations in this gene result in dihydropyrimidine dehydrogenase deficiency, an error in pyrimidine metabolism associated with thymine-uraciluria and an increased risk of toxicity in cancer patients receiving 5-fluorouracil chemotherapy. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009]

DPYD Gene-Disease associations (from GenCC):

• dihydropyrimidine dehydrogenase deficiency

  Inheritance: AR Classification: DEFINITIVE Submitted by: G2P

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000110.4. 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
	DPYD	NM_000110.4	MANE Select	c.851-18506A>G		intron	N/A	NP_000101.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPYD	ENST00000370192.8	TSL:1 MANE Select	c.851-18506A>G		intron	N/A	ENSP00000359211.3

Frequencies

GnomAD3 genomes AF: 0.704 AC: 106757 AN: 151726 Hom.: 38575 Cov.: 32

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.703 AC: 106794 AN: 151844 Hom.: 38586 Cov.: 32 AF XY: 0.704 AC XY: 52249 AN XY: 74188

African (AFR) AF: 0.530 AC: 21927 AN: 41410

American (AMR) AF: 0.797 AC: 12127 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2431 AN: 3470

East Asian (EAS) AF: 0.742 AC: 3824 AN: 5156

South Asian (SAS) AF: 0.798 AC: 3845 AN: 4818

European-Finnish (FIN) AF: 0.740 AC: 7812 AN: 10558

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52456 AN: 67892

Other (OTH) AF: 0.722 AC: 1524 AN: 2110

Alfa AF: 0.750 Hom.: 117413

Bravo AF: 0.703

Asia WGS AF: 0.741 AC: 2576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.74
PhyloP100		0.25
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: rs7533902; hg19: chr1-98079228;