10-7202245-A-T

Variant names:

• chr10-7202245-A-T
• rs2147289
• NM_001387889.1:c.1487+235T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001387889.1(SFMBT2):​c.1487+235T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SFMBT2 NM_001387889.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.855
• Publications: 0 publications found

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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFMBT2	NM_001387889.1	MANE Select	c.1487+235T>A		intron	N/A	NP_001374818.1
	SFMBT2	NM_001018039.1		c.1487+235T>A		intron	N/A	NP_001018049.1
	SFMBT2	NM_001029880.3		c.1487+235T>A		intron	N/A	NP_001025051.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFMBT2	ENST00000397167.6	TSL:5 MANE Select	c.1487+235T>A		intron	N/A	ENSP00000380353.1
	SFMBT2	ENST00000361972.8	TSL:1	c.1487+235T>A		intron	N/A	ENSP00000355109.4
	SFMBT2	ENST00000673876.1		c.1484+235T>A		intron	N/A	ENSP00000501299.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 98686 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 45468

African (AFR) AF: 0.00 AC: 0 AN: 2324

American (AMR) AF: 0.00 AC: 0 AN: 162

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 568

East Asian (EAS) AF: 0.00 AC: 0 AN: 480

South Asian (SAS) AF: 0.00 AC: 0 AN: 2044

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 30

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 186

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 89706

Other (OTH) AF: 0.00 AC: 0 AN: 3186

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.75
DANN	Benign	0.58
PhyloP100		-0.85

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

Other links and lift over

dbSNP: rs2147289; hg19: chr10-7244207;