rs1927060

chrX-80283796-C-A

Variant summary

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

The NR_110646.1(CHMP1B2P):n.665+5110G>T 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 0.548 in 109,728 control chromosomes in the GnomAD database, including 13,222 homozygotes. There are 17,063 hemizygotes in GnomAD. 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 0.55 (13222 hom., 17063 hem., cov: 21)
• Consequence: CHMP1B2P NR_110646.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540

Genes affected

CHMP1B2P (HGNC:49380): (charged multivesicular body protein 1B2, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHMP1B2P	NR_110646.1	n.665+5110G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHMP1B2P	ENST00000399581.4	n.436-1181G>T		intron_variant, non_coding_transcript_variant
CHMP1B2P	ENST00000614414.4	n.711+5110G>T		intron_variant, non_coding_transcript_variant		1
CHMP1B2P	ENST00000691907.1	n.505+5868G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.548 AC: 60101 AN: 109675 Hom.: 13230 Cov.: 21 AF XY: 0.533 AC XY: 17043 AN XY: 31971

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.528

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.0807

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.548 AC: 60110 AN: 109728 Hom.: 13222 Cov.: 21 AF XY: 0.533 AC XY: 17063 AN XY: 32032

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.0812

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.539

Alfa AF: 0.620 Hom.: 5880

Bravo AF: 0.535

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.0
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1927060; hg19: chrX-79539295;