rs10520872

Variant names:

• chr5-21673871-A-G
• rs10520872
• ENST00000522350.1:n.476+49761A>G

Variant summary

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

The ENST00000522350.1(GUSBP1):​n.476+49761A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,002 control chromosomes in the GnomAD database, including 1,891 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 0.15 (1891 hom., cov: 32)
• Consequence: GUSBP1 ENST00000522350.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124
• Publications: 5 publications found

Genes affected

GUSBP1 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522350.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GUSBP1	ENST00000522350.1	TSL:1	n.476+49761A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23380 AN: 151884 Hom.: 1888 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.154 AC: 23393 AN: 152002 Hom.: 1891 Cov.: 32 AF XY: 0.151 AC XY: 11256 AN XY: 74312

African (AFR) AF: 0.136 AC: 5659 AN: 41504

American (AMR) AF: 0.133 AC: 2036 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 601 AN: 3468

East Asian (EAS) AF: 0.248 AC: 1282 AN: 5166

South Asian (SAS) AF: 0.124 AC: 598 AN: 4818

European-Finnish (FIN) AF: 0.127 AC: 1344 AN: 10580

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11239 AN: 67894

Other (OTH) AF: 0.186 AC: 392 AN: 2108

Alfa AF: 0.160 Hom.: 1621

Bravo AF: 0.156

Asia WGS AF: 0.184 AC: 634 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.50
PhyloP100		-0.12

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10520872;

hg19: chr5-21673980;