ENST00000522350.1:n.476+49761A>G

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374685	XR_925848.3	n.3831-2238A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GUSBP1	ENST00000522350.1	n.476+49761A>G		intron_variant	Intron 2 of 3	1

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 v4.3

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

Other links and lift over

dbSNP: rs10520872; hg19: chr5-21673980;