rs942434

Variant names:

• chr10-7195045-C-T
• rs942434
• NM_001387889.1:c.1698+2503G>A

Variant summary

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

The NM_001387889.1(SFMBT2):​c.1698+2503G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 152,100 control chromosomes in the GnomAD database, including 7,368 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 0.29 (7368 hom., cov: 33)
• Consequence: SFMBT2 NM_001387889.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23
• Publications: 6 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 (SAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFMBT2	NM_001387889.1	c.1698+2503G>A		intron_variant	Intron 15 of 20	ENST00000397167.6	NP_001374818.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFMBT2	ENST00000397167.6	c.1698+2503G>A		intron_variant	Intron 15 of 20	5	NM_001387889.1	ENSP00000380353.1

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43621 AN: 151982 Hom.: 7375 Cov.: 33

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.287 AC: 43602 AN: 152100 Hom.: 7368 Cov.: 33 AF XY: 0.293 AC XY: 21752 AN XY: 74342

African (AFR) AF: 0.109 AC: 4531 AN: 41508

American (AMR) AF: 0.290 AC: 4434 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1256 AN: 3468

East Asian (EAS) AF: 0.178 AC: 920 AN: 5172

South Asian (SAS) AF: 0.448 AC: 2159 AN: 4824

European-Finnish (FIN) AF: 0.430 AC: 4541 AN: 10568

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24544 AN: 67956

Other (OTH) AF: 0.336 AC: 708 AN: 2110

Alfa AF: 0.313 Hom.: 1694

Bravo AF: 0.263

Asia WGS AF: 0.329 AC: 1141 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	0.0070
DANN	Benign	0.74
PhyloP100		-2.2
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: rs942434; hg19: chr10-7237007; COSMIC: COSV62811773;