Variant 10-7202245-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001387889.1(SFMBT2):c.1487+235T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 250,422 control chromosomes in the GnomAD database, including 30,714 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 0.48 ( 18282 hom., cov: 33)

Exomes 𝑓: 0.50 ( 12432 hom. )

Consequence

SFMBT2
NM_001387889.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.855

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SFMBT2	NM_001387889.1 linkuse as main transcript	c.1487+235T>C		intron_variant		ENST00000397167.6	NP_001374818.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SFMBT2	ENST00000397167.6 linkuse as main transcript	c.1487+235T>C		intron_variant		5	NM_001387889.1	ENSP00000380353.1		Q5VUG0

Frequencies

GnomAD3 genomes

AF:

0.478

AC:

72682

AN:

151948

Hom.:

18277

Cov.:

show subpopulations

Gnomad AFR

AF:

0.360

Gnomad AMI

AF:

0.480

Gnomad AMR

AF:

0.535

Gnomad ASJ

AF:

0.497

Gnomad EAS

AF:

0.854

Gnomad SAS

AF:

0.503

Gnomad FIN

AF:

0.486

Gnomad MID

AF:

0.396

Gnomad NFE

AF:

0.506

Gnomad OTH

AF:

0.474

GnomAD4 exome

AF:

0.500

AC:

49165

AN:

98356

Hom.:

12432

Cov.:

AF XY:

0.501

AC XY:

22683

AN XY:

45320

show subpopulations

Gnomad4 AFR exome

AF:

0.331

Gnomad4 AMR exome

AF:

0.562

Gnomad4 ASJ exome

AF:

0.514

Gnomad4 EAS exome

AF:

0.831

Gnomad4 SAS exome

AF:

0.477

Gnomad4 FIN exome

AF:

0.467

Gnomad4 NFE exome

AF:

0.502

Gnomad4 OTH exome

AF:

0.521

GnomAD4 genome

AF:

0.478

AC:

72723

AN:

152066

Hom.:

18282

Cov.:

AF XY:

0.481

AC XY:

35747

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.360

Gnomad4 AMR

AF:

0.536

Gnomad4 ASJ

AF:

0.497

Gnomad4 EAS

AF:

0.855

Gnomad4 SAS

AF:

0.505

Gnomad4 FIN

AF:

0.486

Gnomad4 NFE

AF:

0.506

Gnomad4 OTH

AF:

0.473

Alfa

AF:

0.497

Hom.:

24071

Bravo

AF:

0.481

Asia WGS

AF:

0.606

AC:

2106

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.80

DANN

Benign

0.32

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over