dbSNP rs7080643: SFMBT2:c.773-337G>T (chr10-7277326-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001387889.1(SFMBT2):c.773-337G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 214,282 control chromosomes in the GnomAD database, including 43,056 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 0.65 ( 34207 hom., cov: 31)

Exomes 𝑓: 0.53 ( 8849 hom. )

Consequence

SFMBT2
NM_001387889.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.369

Publications

3 publications found

Variant links:

Genes affected

SFMBT2 (HGNC:20256): (Scm like with four mbt domains 2) Enables histone binding activity. Involved in negative regulation of gene expression. Located in aggresome; cytosol; and nuclear speck. [provided by Alliance of Genome Resources, Apr 2022]

SFMBT2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001387889.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SFMBT2	NM_001387889.1	MANE Select	c.773-337G>T	intron	N/A	NP_001374818.1	Q5VUG0
SFMBT2	NM_001018039.1		c.773-337G>T	intron	N/A	NP_001018049.1	Q5VUG0
SFMBT2	NM_001029880.3		c.773-337G>T	intron	N/A	NP_001025051.1	Q5VUG0

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SFMBT2	ENST00000397167.6	TSL:5 MANE Select	c.773-337G>T	intron	N/A	ENSP00000380353.1	Q5VUG0
SFMBT2	ENST00000361972.8	TSL:1	c.773-337G>T	intron	N/A	ENSP00000355109.4	Q5VUG0
SFMBT2	ENST00000673876.1		c.770-337G>T	intron	N/A	ENSP00000501299.1	A0A669KBL2

Frequencies

GnomAD3 genomes

AF:

0.652

AC:

98857

AN:

151638

Hom.:

34148

Cov.:

show subpopulations

Gnomad AFR

AF:

0.884

Gnomad AMI

AF:

0.518

Gnomad AMR

AF:

0.693

Gnomad ASJ

AF:

0.527

Gnomad EAS

AF:

0.777

Gnomad SAS

AF:

0.405

Gnomad FIN

AF:

0.633

Gnomad MID

AF:

0.481

Gnomad NFE

AF:

0.523

Gnomad OTH

AF:

0.591

GnomAD4 exome

AF:

0.526

AC:

32903

AN:

62524

Hom.:

8849

AF XY:

0.524

AC XY:

15316

AN XY:

29238

show subpopulations

African (AFR)

AF:

0.903

AC:

1300

AN:

1440

American (AMR)

AF:

0.604

AC:

AN:

106

Ashkenazi Jewish (ASJ)

AF:

0.532

AC:

184

AN:

346

East Asian (EAS)

AF:

0.770

AC:

228

AN:

296

South Asian (SAS)

AF:

0.363

AC:

479

AN:

1318

European-Finnish (FIN)

AF:

0.550

AC:

AN:

Middle Eastern (MID)

AF:

0.398

AC:

AN:

118

European-Non Finnish (NFE)

AF:

0.519

AC:

29541

AN:

56922

Other (OTH)

AF:

0.536

AC:

1049

AN:

1958

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

720

1440

2161

2881

3601

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1200

2400

3600

4800

6000

<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:

0.652

AC:

98972

AN:

151758

Hom.:

34207

Cov.:

AF XY:

0.653

AC XY:

48435

AN XY:

74166

show subpopulations

African (AFR)

AF:

0.884

AC:

36672

AN:

41490

American (AMR)

AF:

0.693

AC:

10591

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.527

AC:

1820

AN:

3454

East Asian (EAS)

AF:

0.777

AC:

4018

AN:

5168

South Asian (SAS)

AF:

0.404

AC:

1911

AN:

4734

European-Finnish (FIN)

AF:

0.633

AC:

6639

AN:

10494

Middle Eastern (MID)

AF:

0.473

AC:

139

AN:

294

European-Non Finnish (NFE)

AF:

0.523

AC:

35478

AN:

67838

Other (OTH)

AF:

0.587

AC:

1236

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1565

3129

4694

6258

7823

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

762

1524

2286

3048

3810

<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:

0.520

Hom.:

4104

Bravo

AF:

0.673

Asia WGS

AF:

0.574

AC:

1998

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.018

(source)

DANN

Benign

0.56

PhyloP100

-0.37

Mutation Taster

=100/0

polymorphism (auto)

(source)

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