10-7187477-T-C

Variant names:

• chr10-7187477-T-C
• rs2762608
• NM_001387889.1:c.1808+1147A>G

Variant summary

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

The NM_001387889.1(SFMBT2):​c.1808+1147A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 152,214 control chromosomes in the GnomAD database, including 9,186 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 0.31 (9186 hom., cov: 33)
• Consequence: SFMBT2 NM_001387889.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.435 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.1808+1147A>G		intron	N/A	NP_001374818.1
	SFMBT2	NM_001018039.1		c.1808+1147A>G		intron	N/A	NP_001018049.1
	SFMBT2	NM_001029880.3		c.1808+1147A>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.1808+1147A>G		intron	N/A	ENSP00000380353.1
	SFMBT2	ENST00000361972.8	TSL:1	c.1808+1147A>G		intron	N/A	ENSP00000355109.4
	SFMBT2	ENST00000673876.1		c.1805+1147A>G		intron	N/A	ENSP00000501299.1

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47449 AN: 152096 Hom.: 9192 Cov.: 33

Gnomad AFR AF: 0.0888

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.312 AC: 47430 AN: 152214 Hom.: 9186 Cov.: 33 AF XY: 0.317 AC XY: 23619 AN XY: 74426

African (AFR) AF: 0.0886 AC: 3682 AN: 41568

American (AMR) AF: 0.339 AC: 5181 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1364 AN: 3472

East Asian (EAS) AF: 0.179 AC: 925 AN: 5178

South Asian (SAS) AF: 0.450 AC: 2175 AN: 4828

European-Finnish (FIN) AF: 0.468 AC: 4956 AN: 10580

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27772 AN: 67978

Other (OTH) AF: 0.355 AC: 751 AN: 2114

Alfa AF: 0.345 Hom.: 1685

Bravo AF: 0.289

Asia WGS AF: 0.335 AC: 1164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.016
DANN	Benign	0.41
PhyloP100		-1.5
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: rs2762608; hg19: chr10-7229439;