2-3701381-T-C

Position:

• chr2-3701381-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018436.4(ALLC):​c.851-131T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0964 in 1,124,190 control chromosomes in the GnomAD database, including 6,224 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 0.13 (1652 hom., cov: 32)
  • Exomes 𝑓: 0.091 (4572 hom.)
• Consequence: ALLC NM_018436.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640

Genes affected

ALLC (HGNC:17377): (allantoicase) Allantoicase (EC 3.5.3.4) participates in the uric acid degradation pathway. Its enzymatic activity, like that of urate oxidase (MIM 191540), was lost during vertebrate evolution.[supplied by OMIM, Nov 2008]

ALLC (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALLC	NM_018436.4	c.851-131T>C		intron_variant		ENST00000252505.4	NP_060906.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALLC	ENST00000252505.4	c.851-131T>C		intron_variant		1	NM_018436.4	ENSP00000252505.3
ALLC	ENST00000471711.1	n.515-131T>C		intron_variant		3
ALLC	ENST00000476389.5	n.1436-131T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19913 AN: 152106 Hom.: 1644 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.0916

Gnomad ASJ AF: 0.0854

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0323

Gnomad FIN AF: 0.0741

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0953

Gnomad OTH AF: 0.133

GnomAD4 exome AF: 0.0910 AC: 88457 AN: 971966 Hom.: 4572 AF XY: 0.0889 AC XY: 42586 AN XY: 478816

Gnomad4 AFR exome AF: 0.231

Gnomad4 AMR exome AF: 0.0658

Gnomad4 ASJ exome AF: 0.0814

Gnomad4 EAS exome AF: 0.0864

Gnomad4 SAS exome AF: 0.0253

Gnomad4 FIN exome AF: 0.0751

Gnomad4 NFE exome AF: 0.0931

Gnomad4 OTH exome AF: 0.0943

GnomAD4 genome AF: 0.131 AC: 19951 AN: 152224 Hom.: 1652 Cov.: 32 AF XY: 0.127 AC XY: 9467 AN XY: 74428

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.0913

Gnomad4 ASJ AF: 0.0854

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.0321

Gnomad4 FIN AF: 0.0741

Gnomad4 NFE AF: 0.0953

Gnomad4 OTH AF: 0.133

Alfa AF: 0.0968 Hom.: 988

Bravo AF: 0.140

Asia WGS AF: 0.0870 AC: 302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.3
DANN	Benign	0.81

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

Publications

LitVar

Other links and lift over

dbSNP: rs6730148; hg19: chr2-3748971;