rs1822841

Positions:

• chr4-143921485-T-G

Variant summary

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

The NR_125886.1(LOC101927636):​n.218+8847T>G variant causes a intron, non coding transcript 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: LOC101927636 NR_125886.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590

Genes affected

GUSBP5 (HGNC:42319): (GUSB pseudogene 5)

LOC101927636 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927636	NR_125886.1	n.218+8847T>G		intron_variant, non_coding_transcript_variant
LOC105377459	XR_001741861.1	n.1464-47767T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GUSBP5	ENST00000509873.5	n.218+8847T>G		intron_variant, non_coding_transcript_variant		1
GUSBP5	ENST00000641556.1	n.357-45603T>G		intron_variant, non_coding_transcript_variant
GUSBP5	ENST00000641676.1	n.302-51625T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0911

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.0465

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.257

Alfa AF: 0.309 Hom.: 3817

Bravo AF: 0.237

Asia WGS AF: 0.197 AC: 689 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.1
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1822841; hg19: chr4-144842638;