20-2840955-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_022575.4(VPS16):​c.53+128C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 907,542 control chromosomes in the GnomAD database, including 14,465 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.22 ( 5352 hom., cov: 32)
Exomes 𝑓: 0.14 ( 9113 hom. )

Consequence

VPS16
NM_022575.4 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.567
Variant links:
Genes affected
VPS16 (HGNC:14584): (VPS16 core subunit of CORVET and HOPS complexes) Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinct organelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved in vesicle transport to vacuoles. This gene encodes the human homolog of yeast class C Vps16 protein. The mammalian class C Vps proteins are predominantly associated with late endosomes/lysosomes, and like their yeast counterparts, may mediate vesicle trafficking steps in the endosome/lysosome pathway. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2009]
PCED1A (HGNC:16212): (PC-esterase domain containing 1A) The protein encoded by this gene is a member of the GDSL/SGNH superfamily. Members of this family are hydrolytic enzymes with esterase and lipase activity and broad substrate specificity. This protein belongs to the Pmr5-Cas1p-esterase subfamily in that it contains the catalytic triad comprised of serine, aspartate and histidine and lacks two conserved regions (glycine after strand S2 and GxND motif). A pseudogene of this gene has been identified on the long arm of chromosome 2. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, Sep 2012]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 20-2840955-C-T is Benign according to our data. Variant chr20-2840955-C-T is described in ClinVar as [Benign]. Clinvar id is 1286534.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
VPS16NM_022575.4 linkuse as main transcriptc.53+128C>T intron_variant ENST00000380445.8 NP_072097.2
PCED1ANM_001271168.2 linkuse as main transcriptc.-111G>A 5_prime_UTR_variant 1/8 NP_001258097.1
PCED1AXM_005260804.3 linkuse as main transcriptc.-111G>A 5_prime_UTR_variant 1/8 XP_005260861.1
VPS16NM_080413.3 linkuse as main transcriptc.53+128C>T intron_variant NP_536338.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
VPS16ENST00000380445.8 linkuse as main transcriptc.53+128C>T intron_variant 1 NM_022575.4 ENSP00000369810 P1Q9H269-1

Frequencies

GnomAD3 genomes
AF:
0.224
AC:
34080
AN:
152028
Hom.:
5348
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.447
Gnomad AMI
AF:
0.0998
Gnomad AMR
AF:
0.193
Gnomad ASJ
AF:
0.0864
Gnomad EAS
AF:
0.129
Gnomad SAS
AF:
0.107
Gnomad FIN
AF:
0.148
Gnomad MID
AF:
0.0506
Gnomad NFE
AF:
0.134
Gnomad OTH
AF:
0.177
GnomAD4 exome
AF:
0.143
AC:
108374
AN:
755402
Hom.:
9113
Cov.:
10
AF XY:
0.140
AC XY:
53922
AN XY:
383930
show subpopulations
Gnomad4 AFR exome
AF:
0.454
Gnomad4 AMR exome
AF:
0.216
Gnomad4 ASJ exome
AF:
0.0754
Gnomad4 EAS exome
AF:
0.162
Gnomad4 SAS exome
AF:
0.105
Gnomad4 FIN exome
AF:
0.149
Gnomad4 NFE exome
AF:
0.136
Gnomad4 OTH exome
AF:
0.143
GnomAD4 genome
AF:
0.224
AC:
34108
AN:
152140
Hom.:
5352
Cov.:
32
AF XY:
0.221
AC XY:
16445
AN XY:
74394
show subpopulations
Gnomad4 AFR
AF:
0.446
Gnomad4 AMR
AF:
0.193
Gnomad4 ASJ
AF:
0.0864
Gnomad4 EAS
AF:
0.129
Gnomad4 SAS
AF:
0.107
Gnomad4 FIN
AF:
0.148
Gnomad4 NFE
AF:
0.134
Gnomad4 OTH
AF:
0.174
Alfa
AF:
0.181
Hom.:
675
Bravo
AF:
0.239
Asia WGS
AF:
0.116
AC:
402
AN:
3476

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxMay 17, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
8.0
DANN
Benign
0.84

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2297047; hg19: chr20-2821601; API