Variant rs2462712 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.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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0770

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=-0.89).

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/exons	MANE	Protein	UniProt
SFMBT2	NM_001387889.1 linkuse as main transcript	c.1808+62C>A		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.1808+62C>A		intron_variant		5	NM_001387889.1	ENSP00000380353.1		Q5VUG0

Frequencies

GnomAD3 genomes

AF:

0.615

AC:

93399

AN:

151922

Hom.:

29421

Cov.:

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

Gnomad4 AFR exome

AF:

0.669

Gnomad4 AMR exome

AF:

0.501

Gnomad4 ASJ exome

AF:

0.580

Gnomad4 EAS exome

AF:

0.169

Gnomad4 SAS exome

AF:

0.576

Gnomad4 FIN exome

AF:

0.628

Gnomad4 NFE exome

AF:

0.631

Gnomad4 OTH exome

AF:

0.597

GnomAD4 genome

AF:

0.615

AC:

93480

AN:

152040

Hom.:

29454

Cov.:

AF XY:

0.611

AC XY:

45436

AN XY:

74304

show subpopulations

Gnomad4 AFR

AF:

0.669

Gnomad4 AMR

AF:

0.580

Gnomad4 ASJ

AF:

0.584

Gnomad4 EAS

AF:

0.181

Gnomad4 SAS

AF:

0.560

Gnomad4 FIN

AF:

0.632

Gnomad4 NFE

AF:

0.623

Gnomad4 OTH

AF:

0.623

Alfa

AF:

0.618

Hom.:

39646

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

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