rs1924504

Variant names:

• chr10-7241804-A-C
• rs1924504
• NM_001387889.1:c.1120+1754T>G

Your query was ambiguous. Multiple possible variants found:

• chr10-7241804-A-C
• chr10-7241804-A-G
• chr10-7241804-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001387889.1(SFMBT2):​c.1120+1754T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,964 control chromosomes in the GnomAD database, including 18,012 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 (18012 hom., cov: 32)
• Consequence: SFMBT2 NM_001387889.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.565
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFMBT2	NM_001387889.1	MANE Select	c.1120+1754T>G		intron	N/A	NP_001374818.1
	SFMBT2	NM_001018039.1		c.1120+1754T>G		intron	N/A	NP_001018049.1
	SFMBT2	NM_001029880.3		c.1120+1754T>G		intron	N/A	NP_001025051.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFMBT2	ENST00000397167.6	TSL:5 MANE Select	c.1120+1754T>G		intron	N/A	ENSP00000380353.1
	SFMBT2	ENST00000361972.8	TSL:1	c.1120+1754T>G		intron	N/A	ENSP00000355109.4
	SFMBT2	ENST00000673876.1		c.1117+1754T>G		intron	N/A	ENSP00000501299.1

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72362 AN: 151846 Hom.: 18016 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.466

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.476 AC: 72387 AN: 151964 Hom.: 18012 Cov.: 32 AF XY: 0.477 AC XY: 35427 AN XY: 74280

African (AFR) AF: 0.369 AC: 15309 AN: 41460

American (AMR) AF: 0.470 AC: 7168 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1861 AN: 3472

East Asian (EAS) AF: 0.855 AC: 4424 AN: 5172

South Asian (SAS) AF: 0.383 AC: 1844 AN: 4814

European-Finnish (FIN) AF: 0.549 AC: 5784 AN: 10528

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.506 AC: 34397 AN: 67944

Other (OTH) AF: 0.464 AC: 981 AN: 2116

Alfa AF: 0.475 Hom.: 3005

Bravo AF: 0.477

Asia WGS AF: 0.569 AC: 1971 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.64
PhyloP100		0.56
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

Other links and lift over

dbSNP: rs1924504; hg19: chr10-7283766;