NM_001387889.1:c.1808+62C>A

Variant summary

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

The NM_001387889.1(SFMBT2):​c.1808+62C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 1,360,230 control chromosomes in the GnomAD database, including 256,565 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 0.61 ( 29454 hom., cov: 32)
Exomes 𝑓: 0.61 ( 227111 hom. )

Consequence

SFMBT2
NM_001387889.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0770

Publications

7 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]

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=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SFMBT2NM_001387889.1 linkc.1808+62C>A intron_variant Intron 16 of 20 ENST00000397167.6 NP_001374818.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SFMBT2ENST00000397167.6 linkc.1808+62C>A intron_variant Intron 16 of 20 5 NM_001387889.1 ENSP00000380353.1 Q5VUG0

Frequencies

GnomAD3 genomes
AF:
0.615
AC:
93399
AN:
151922
Hom.:
29421
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.668
Gnomad AMI
AF:
0.782
Gnomad AMR
AF:
0.581
Gnomad ASJ
AF:
0.584
Gnomad EAS
AF:
0.181
Gnomad SAS
AF:
0.561
Gnomad FIN
AF:
0.632
Gnomad MID
AF:
0.633
Gnomad NFE
AF:
0.623
Gnomad OTH
AF:
0.622
GnomAD4 exome
AF:
0.607
AC:
732871
AN:
1208190
Hom.:
227111
AF XY:
0.605
AC XY:
368710
AN XY:
609834
show subpopulations
African (AFR)
AF:
0.669
AC:
18929
AN:
28288
American (AMR)
AF:
0.501
AC:
20464
AN:
40856
Ashkenazi Jewish (ASJ)
AF:
0.580
AC:
13449
AN:
23172
East Asian (EAS)
AF:
0.169
AC:
6460
AN:
38230
South Asian (SAS)
AF:
0.576
AC:
44503
AN:
77222
European-Finnish (FIN)
AF:
0.628
AC:
31818
AN:
50690
Middle Eastern (MID)
AF:
0.619
AC:
3030
AN:
4898
European-Non Finnish (NFE)
AF:
0.631
AC:
563251
AN:
892960
Other (OTH)
AF:
0.597
AC:
30967
AN:
51874
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
13265
26529
39794
53058
66323
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
13826
27652
41478
55304
69130
<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:
0.615
AC:
93480
AN:
152040
Hom.:
29454
Cov.:
32
AF XY:
0.611
AC XY:
45436
AN XY:
74304
show subpopulations
African (AFR)
AF:
0.669
AC:
27729
AN:
41456
American (AMR)
AF:
0.580
AC:
8865
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
0.584
AC:
2026
AN:
3472
East Asian (EAS)
AF:
0.181
AC:
936
AN:
5174
South Asian (SAS)
AF:
0.560
AC:
2694
AN:
4814
European-Finnish (FIN)
AF:
0.632
AC:
6662
AN:
10544
Middle Eastern (MID)
AF:
0.633
AC:
186
AN:
294
European-Non Finnish (NFE)
AF:
0.623
AC:
42358
AN:
67988
Other (OTH)
AF:
0.623
AC:
1311
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1783
3566
5348
7131
8914
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
766
1532
2298
3064
3830
<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:
0.618
Hom.:
46937
Bravo
AF:
0.609
Asia WGS
AF:
0.423
AC:
1471
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.7
DANN
Benign
0.45
PhyloP100
0.077
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs2462712; hg19: chr10-7230524; COSMIC: COSV62806884; API