NM_152272.5:c.472-2257C>T

Variant names:

• chr8-23252990-C-T
• rs11135712
• NM_152272.5:c.472-2257C>T

Variant summary

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

The NM_152272.5(CHMP7):​c.472-2257C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 152,096 control chromosomes in the GnomAD database, including 9,522 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 0.34 (9522 hom., cov: 32)
• Consequence: CHMP7 NM_152272.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.641
• Publications: 7 publications found

Genes affected

CHMP7 (HGNC:28439): (charged multivesicular body protein 7) Involved in several processes, including late endosome to vacuole transport; midbody abscission; and mitotic nuclear division. Located in cytosol; nuclear envelope; and nucleoplasm. Part of ESCRT III complex. Colocalizes with chromatin. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHMP7	NM_152272.5	c.472-2257C>T		intron_variant	Intron 3 of 10	ENST00000397677.6	NP_689485.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHMP7	ENST00000397677.6	c.472-2257C>T		intron_variant	Intron 3 of 10	1	NM_152272.5	ENSP00000380794.1

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51101 AN: 151976 Hom.: 9507 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.336 AC: 51138 AN: 152096 Hom.: 9522 Cov.: 32 AF XY: 0.341 AC XY: 25324 AN XY: 74354

African (AFR) AF: 0.162 AC: 6743 AN: 41516

American (AMR) AF: 0.411 AC: 6276 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1560 AN: 3466

East Asian (EAS) AF: 0.331 AC: 1713 AN: 5178

South Asian (SAS) AF: 0.474 AC: 2280 AN: 4814

European-Finnish (FIN) AF: 0.395 AC: 4183 AN: 10580

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27173 AN: 67950

Other (OTH) AF: 0.347 AC: 733 AN: 2114

Alfa AF: 0.388 Hom.: 10207

Bravo AF: 0.325

Asia WGS AF: 0.419 AC: 1459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.56
PhyloP100		-0.64
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs11135712; hg19: chr8-23110503;