rs1899965

Variant names:

• chr4-143867045-T-C
• rs1899965
• ENST00000641328.2:n.1316+969T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000641328.2(GUSBP5):​n.1316+969T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0168 in 152,240 control chromosomes in the GnomAD database, including 36 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 0.017 (36 hom., cov: 33)
• Consequence: GUSBP5 ENST00000641328.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639
• Publications: 0 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=-1.02).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0168 (2563/152240) while in subpopulation NFE AF = 0.0244 (1657/68008). AF 95% confidence interval is 0.0234. There are 36 homozygotes in GnomAd4. There are 1234 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 36 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377459	XR_001741861.1	n.1463+969T>C		intron_variant	Intron 9 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GUSBP5	ENST00000641328.2	n.1316+969T>C		intron_variant	Intron 6 of 6
GUSBP5	ENST00000641556.1	n.356+969T>C		intron_variant	Intron 3 of 7
GUSBP5	ENST00000641676.2	n.636+969T>C		intron_variant	Intron 6 of 8

Frequencies

GnomAD3 genomes AF: 0.0168 AC: 2563 AN: 152122 Hom.: 36 Cov.: 33

Gnomad AFR AF: 0.00478

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0146

Gnomad ASJ AF: 0.0329

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00290

Gnomad FIN AF: 0.0201

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0244

Gnomad OTH AF: 0.0163

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

GnomAD4 genome AF: 0.0168 AC: 2563 AN: 152240 Hom.: 36 Cov.: 33 AF XY: 0.0166 AC XY: 1234 AN XY: 74428

African (AFR) AF: 0.00477 AC: 198 AN: 41548

American (AMR) AF: 0.0146 AC: 223 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0329 AC: 114 AN: 3468

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5180

South Asian (SAS) AF: 0.00291 AC: 14 AN: 4816

European-Finnish (FIN) AF: 0.0201 AC: 213 AN: 10618

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0244 AC: 1657 AN: 68008

Other (OTH) AF: 0.0161 AC: 34 AN: 2112

Alfa AF: 0.0212 Hom.: 4

Bravo AF: 0.0160

Asia WGS AF: 0.00289 AC: 10 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.3
DANN	Benign	0.55
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs1899965; hg19: chr4-144788198;