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GeneBe

2-54255840-C-A

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_001003937.3(TSPYL6):c.312G>T(p.Ser104=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00123 in 1,613,926 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0018 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 1 hom. )

Consequence

TSPYL6
NM_001003937.3 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.46
Variant links:
Genes affected
TSPYL6 (HGNC:14521): (TSPY like 6) Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in nucleosome assembly. Predicted to be active in chromatin and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
ACYP2 (HGNC:180): (acylphosphatase 2) Acylphosphatase can hydrolyze the phosphoenzyme intermediate of different membrane pumps, particularly the Ca2+/Mg2+-ATPase from sarcoplasmic reticulum of skeletal muscle. Two isoenzymes have been isolated, called muscle acylphosphatase and erythrocyte acylphosphatase on the basis of their tissue localization. This gene encodes the muscle-type isoform (MT). An increase of the MT isoform is associated with muscle differentiation. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 2-54255840-C-A is Benign according to our data. Variant chr2-54255840-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 775170.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.46 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TSPYL6NM_001003937.3 linkuse as main transcriptc.312G>T p.Ser104= synonymous_variant 1/1 ENST00000317802.9
ACYP2NM_001320586.2 linkuse as main transcriptc.405-48848C>A intron_variant ENST00000607452.6
LOC105374610XR_007086321.1 linkuse as main transcriptn.1296-16556G>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TSPYL6ENST00000317802.9 linkuse as main transcriptc.312G>T p.Ser104= synonymous_variant 1/1 NM_001003937.3 P1
ACYP2ENST00000607452.6 linkuse as main transcriptc.405-48848C>A intron_variant 2 NM_001320586.2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00183
AC:
279
AN:
152096
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00246
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00183
Gnomad ASJ
AF:
0.00259
Gnomad EAS
AF:
0.000194
Gnomad SAS
AF:
0.000829
Gnomad FIN
AF:
0.000849
Gnomad MID
AF:
0.0223
Gnomad NFE
AF:
0.00154
Gnomad OTH
AF:
0.00670
GnomAD3 exomes
AF:
0.00138
AC:
344
AN:
249338
Hom.:
0
AF XY:
0.00151
AC XY:
205
AN XY:
135316
show subpopulations
Gnomad AFR exome
AF:
0.00258
Gnomad AMR exome
AF:
0.00116
Gnomad ASJ exome
AF:
0.00179
Gnomad EAS exome
AF:
0.0000556
Gnomad SAS exome
AF:
0.00118
Gnomad FIN exome
AF:
0.000187
Gnomad NFE exome
AF:
0.00170
Gnomad OTH exome
AF:
0.00215
GnomAD4 exome
AF:
0.00117
AC:
1704
AN:
1461714
Hom.:
1
Cov.:
36
AF XY:
0.00120
AC XY:
870
AN XY:
727170
show subpopulations
Gnomad4 AFR exome
AF:
0.00236
Gnomad4 AMR exome
AF:
0.00136
Gnomad4 ASJ exome
AF:
0.00176
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00118
Gnomad4 FIN exome
AF:
0.000319
Gnomad4 NFE exome
AF:
0.00115
Gnomad4 OTH exome
AF:
0.00142
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00183
AC:
278
AN:
152212
Hom.:
1
Cov.:
32
AF XY:
0.00173
AC XY:
129
AN XY:
74412
show subpopulations
Gnomad4 AFR
AF:
0.00248
Gnomad4 AMR
AF:
0.00183
Gnomad4 ASJ
AF:
0.00259
Gnomad4 EAS
AF:
0.000194
Gnomad4 SAS
AF:
0.000830
Gnomad4 FIN
AF:
0.000849
Gnomad4 NFE
AF:
0.00153
Gnomad4 OTH
AF:
0.00663
Alfa
AF:
0.00115
Hom.:
0
Bravo
AF:
0.00190
Asia WGS
AF:
0.000866
AC:
3
AN:
3478
EpiCase
AF:
0.00191
EpiControl
AF:
0.00273

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingInvitaeSep 07, 2017- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.68
Cadd
Benign
0.44
Dann
Benign
0.52

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: rs114346583; hg19: chr2-54482977; API