chrX-16170676-GTCC-G

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PM4_SupportingBP6_ModerateBS2

The NM_001277307.2(MAGEB17):​c.300_302delCTC​(p.Ser101del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000317 in 1,165,644 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 119 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00021 ( 0 hom., 6 hem., cov: 23)
Exomes 𝑓: 0.00033 ( 0 hom. 113 hem. )

Consequence

MAGEB17
NM_001277307.2 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.13
Variant links:
Genes affected
MAGEB17 (HGNC:17418): (MAGE family member B17) Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
ENSG00000238178 (HGNC:56739): (MAGEB17 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

PM4
Nonframeshift variant in NON repetitive region in NM_001277307.2. Strenght limited to Supporting due to length of the change: 1aa.
BP6
Variant X-16170676-GTCC-G is Benign according to our data. Variant chrX-16170676-GTCC-G is described in ClinVar as [Likely_benign]. Clinvar id is 2660064.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Hemizygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MAGEB17NM_001277307.2 linkc.300_302delCTC p.Ser101del disruptive_inframe_deletion Exon 2 of 2 ENST00000400004.6 NP_001264236.1 A8MXT2
MAGEB17XM_047442355.1 linkc.300_302delCTC p.Ser101del disruptive_inframe_deletion Exon 2 of 2 XP_047298311.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MAGEB17ENST00000400004.6 linkc.300_302delCTC p.Ser101del disruptive_inframe_deletion Exon 2 of 2 2 NM_001277307.2 ENSP00000382884.2 A8MXT2
MAGEB17ENST00000400003.1 linkc.300_302delCTC p.Ser101del disruptive_inframe_deletion Exon 3 of 3 5 ENSP00000382883.1 A8MXT2
ENSG00000238178ENST00000435789.1 linkn.191_193delGGA non_coding_transcript_exon_variant Exon 1 of 6 5

Frequencies

GnomAD3 genomes
AF:
0.000214
AC:
24
AN:
112207
Hom.:
0
Cov.:
23
AF XY:
0.000175
AC XY:
6
AN XY:
34381
show subpopulations
Gnomad AFR
AF:
0.000130
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000376
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000175
AC:
19
AN:
108382
Hom.:
0
AF XY:
0.000303
AC XY:
12
AN XY:
39610
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000712
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000430
Gnomad OTH exome
AF:
0.000313
GnomAD4 exome
AF:
0.000328
AC:
346
AN:
1053385
Hom.:
0
AF XY:
0.000328
AC XY:
113
AN XY:
344741
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000358
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000200
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000410
Gnomad4 OTH exome
AF:
0.000180
GnomAD4 genome
AF:
0.000214
AC:
24
AN:
112259
Hom.:
0
Cov.:
23
AF XY:
0.000174
AC XY:
6
AN XY:
34443
show subpopulations
Gnomad4 AFR
AF:
0.000129
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000376
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000260
Hom.:
2
Bravo
AF:
0.000283

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 testingCeGaT Center for Human Genetics TuebingenMar 01, 2023MAGEB17: BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs765679969; hg19: chrX-16188799; API