rs6520141

chr22-49894697-A-G

Variant summary

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

The XM_017028936.2(ALG12):c.1238+9482T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,248 control chromosomes in the GnomAD database, including 9,994 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 0.26 (9994 hom., cov: 33)
• Consequence: ALG12 XM_017028936.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246

Genes affected

ALG12 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALG12	XM_017028936.2	c.1238+9482T>C		intron_variant
ALG12	XM_017028937.2	c.1238+9482T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39082 AN: 152130 Hom.: 9960 Cov.: 33

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.0447

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.0902

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.257 AC: 39166 AN: 152248 Hom.: 9994 Cov.: 33 AF XY: 0.252 AC XY: 18762 AN XY: 74450

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.0447

Gnomad4 NFE AF: 0.0902

Gnomad4 OTH AF: 0.222

Alfa AF: 0.218 Hom.: 1761

Bravo AF: 0.278

Asia WGS AF: 0.201 AC: 697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	3.9
Dann	Benign	0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6520141; hg19: chr22-50288345;