rs1822841

Variant names:

• chr4-143921485-T-G
• rs1822841
• ENST00000509873.5:n.218+8847T>G

Variant summary

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

The ENST00000509873.5(GUSBP5):​n.218+8847T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 150,462 control chromosomes in the GnomAD database, including 5,037 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 0.24 (5037 hom., cov: 32)
• Consequence: GUSBP5 ENST00000509873.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590
• Publications: 17 publications found

Genes affected

GUSBP5 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509873.5. 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
	LOC101927636	NR_125886.1		n.218+8847T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GUSBP5	ENST00000509873.5	TSL:1	n.218+8847T>G		intron	N/A
	GUSBP5	ENST00000641556.1		n.357-45603T>G		intron	N/A
	GUSBP5	ENST00000641676.2		n.637-51625T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36266 AN: 150350 Hom.: 5030 Cov.: 32

Gnomad AFR AF: 0.0908

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.0466

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.298

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.241 AC: 36285 AN: 150462 Hom.: 5037 Cov.: 32 AF XY: 0.243 AC XY: 17843 AN XY: 73474

African (AFR) AF: 0.0911 AC: 3721 AN: 40858

American (AMR) AF: 0.310 AC: 4683 AN: 15104

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1146 AN: 3432

East Asian (EAS) AF: 0.0465 AC: 240 AN: 5164

South Asian (SAS) AF: 0.313 AC: 1489 AN: 4756

European-Finnish (FIN) AF: 0.317 AC: 3305 AN: 10438

Middle Eastern (MID) AF: 0.287 AC: 81 AN: 282

European-Non Finnish (NFE) AF: 0.311 AC: 20944 AN: 67442

Other (OTH) AF: 0.257 AC: 534 AN: 2074

Alfa AF: 0.310 Hom.: 4195

Bravo AF: 0.237

Asia WGS AF: 0.197 AC: 689 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.1
DANN	Benign	0.45
PhyloP100		-0.059
Mutation Taster		=100/0	polymorphism

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: rs1822841;

hg19: chr4-144842638;