Variant rs7080643 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.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

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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.876 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.773-337G>T		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.773-337G>T		intron_variant		5	NM_001387889.1	ENSP00000380353.1		Q5VUG0

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

Gnomad4 AFR exome

AF:

0.903

Gnomad4 AMR exome

AF:

0.604

Gnomad4 ASJ exome

AF:

0.532

Gnomad4 EAS exome

AF:

0.770

Gnomad4 SAS exome

AF:

0.363

Gnomad4 FIN exome

AF:

0.550

Gnomad4 NFE exome

AF:

0.519

Gnomad4 OTH exome

AF:

0.536

GnomAD4 genome

AF:

0.652

AC:

98972

AN:

151758

Hom.:

34207

Cov.:

AF XY:

0.653

AC XY:

48435

AN XY:

74166

show subpopulations

Gnomad4 AFR

AF:

0.884

Gnomad4 AMR

AF:

0.693

Gnomad4 ASJ

AF:

0.527

Gnomad4 EAS

AF:

0.777

Gnomad4 SAS

AF:

0.404

Gnomad4 FIN

AF:

0.633

Gnomad4 NFE

AF:

0.523

Gnomad4 OTH

AF:

0.587

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.018

DANN

Benign

0.56

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