Genetic Variant NM_001396029.1:c.774C>T (chrX-26161374-C-T) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001396029.1(MAGEB6B):c.774C>T(p.Ser258Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000163 in 698,242 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 59 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000099 ( 0 hom., 4 hem., cov: 22)

Exomes 𝑓: 0.00018 ( 0 hom. 55 hem. )

Consequence

MAGEB6B
NM_001396029.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.96

Publications

0 publications found

Variant links:

Genes affected

MAGEB6B (HGNC:28824): (MAGE family member B6B) 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]

MAGEB6B links:

ENSG00000304664 (HGNC:):

ENSG00000304664 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant X-26161374-C-T is Benign according to our data. Variant chrX-26161374-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2660203.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.96 with no splicing effect.

BS2

High Hemizygotes in GnomAd4 at 4 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001396029.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAGEB6B	NM_001396029.1	MANE Select	c.774C>T	p.Ser258Ser	synonymous	Exon 1 of 1	NP_001382958.1	A0A0J9YX57

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAGEB6B	ENST00000416929.3	TSL:6 MANE Select	c.774C>T	p.Ser258Ser	synonymous	Exon 1 of 1	ENSP00000488257.1	A0A0J9YX57
	ENSG00000304664	ENST00000805264.1		n.136-8578G>A		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0000988

AC:

AN:

111282

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000654

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000956

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000769

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000113

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.000175

AC:

AN:

182949

AF XY:

0.000237

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000182

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000135

Gnomad OTH exome

AF:

0.000221

GnomAD4 exome

AF:

0.000175

AC:

103

AN:

586960

Hom.:

Cov.:

AF XY:

0.000291

AC XY:

AN XY:

189096

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

16694

American (AMR)

AF:

0.000202

AC:

AN:

34569

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

16196

East Asian (EAS)

AF:

0.0000359

AC:

AN:

27849

South Asian (SAS)

AF:

0.00119

AC:

AN:

44473

European-Finnish (FIN)

AF:

0.00

AC:

AN:

40217

Middle Eastern (MID)

AF:

0.000309

AC:

AN:

3241

European-Non Finnish (NFE)

AF:

0.000101

AC:

AN:

374572

Other (OTH)

AF:

0.000103

AC:

AN:

29149

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000988

AC:

AN:

111282

Hom.:

Cov.:

AF XY:

0.000119

AC XY:

AN XY:

33484

show subpopulations

African (AFR)

AF:

0.0000654

AC:

AN:

30588

American (AMR)

AF:

0.0000956

AC:

AN:

10461

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2649

East Asian (EAS)

AF:

0.00

AC:

AN:

3518

South Asian (SAS)

AF:

0.000769

AC:

AN:

2600

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5941

Middle Eastern (MID)

AF:

0.00

AC:

AN:

238

European-Non Finnish (NFE)

AF:

0.000113

AC:

AN:

53109

Other (OTH)

AF:

0.00

AC:

AN:

1490

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000130

Hom.:

Bravo

AF:

0.000102

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.48

(source)

DANN

Benign

0.91

PhyloP100

-2.0

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over