2-3701381-T-C

Variant names:

• chr2-3701381-T-C
• rs6730148
• NM_018436.4:c.851-131T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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]

ENSG00000224661 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ALLC	NM_018436.4	c.851-131T>C		intron_variant	Intron 10 of 11	ENST00000252505.4	NP_060906.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALLC	ENST00000252505.4	c.851-131T>C		intron_variant	Intron 10 of 11	1	NM_018436.4	ENSP00000252505.3

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

African (AFR) AF: 0.231 AC: 4974 AN: 21496

American (AMR) AF: 0.0658 AC: 1261 AN: 19178

Ashkenazi Jewish (ASJ) AF: 0.0814 AC: 1279 AN: 15716

East Asian (EAS) AF: 0.0864 AC: 2767 AN: 32042

South Asian (SAS) AF: 0.0253 AC: 1221 AN: 48238

European-Finnish (FIN) AF: 0.0751 AC: 2902 AN: 38642

Middle Eastern (MID) AF: 0.0624 AC: 274 AN: 4392

European-Non Finnish (NFE) AF: 0.0931 AC: 69830 AN: 750370

Other (OTH) AF: 0.0943 AC: 3949 AN: 41892

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

African (AFR) AF: 0.235 AC: 9774 AN: 41510

American (AMR) AF: 0.0913 AC: 1398 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0854 AC: 296 AN: 3466

East Asian (EAS) AF: 0.110 AC: 572 AN: 5180

South Asian (SAS) AF: 0.0321 AC: 155 AN: 4826

European-Finnish (FIN) AF: 0.0741 AC: 786 AN: 10608

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0953 AC: 6480 AN: 68012

Other (OTH) AF: 0.133 AC: 280 AN: 2112

Alfa AF: 0.106 Hom.: 3355

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
PhyloP100		-0.064
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: rs6730148; hg19: chr2-3748971;