rs1927060

Variant names:

• chrX-80283796-C-A
• rs1927060
• ENST00000614414.4:n.711+5110G>T

Variant summary

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

The ENST00000614414.4(CHMP1B2P):​n.711+5110G>T variant causes a intron 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 ENST00000614414.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540
• Publications: 4 publications found

Genes affected

CHMP1B2P (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CHMP1B2P	NR_110646.1	n.665+5110G>T		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHMP1B2P	ENST00000614414.4	n.711+5110G>T		intron_variant	Intron 5 of 5	1
CHMP1B2P	ENST00000399581.4	n.436-1181G>T		intron_variant	Intron 5 of 7	6
CHMP1B2P	ENST00000691907.1	n.505+5868G>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.548 AC: 60101 AN: 109675 Hom.: 13230 Cov.: 21

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

African (AFR) AF: 0.334 AC: 10079 AN: 30215

American (AMR) AF: 0.554 AC: 5636 AN: 10173

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 1685 AN: 2607

East Asian (EAS) AF: 0.0812 AC: 283 AN: 3485

South Asian (SAS) AF: 0.248 AC: 654 AN: 2636

European-Finnish (FIN) AF: 0.614 AC: 3478 AN: 5667

Middle Eastern (MID) AF: 0.580 AC: 120 AN: 207

European-Non Finnish (NFE) AF: 0.704 AC: 37025 AN: 52592

Other (OTH) AF: 0.539 AC: 797 AN: 1478

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
PhyloP100		-0.054

Splicing

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

Other links and lift over

dbSNP: rs1927060; hg19: chrX-79539295;