chr10-7202245-A-G

Variant names:

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

Variant summary

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

The NM_001387889.1(SFMBT2):​c.1487+235T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 250,422 control chromosomes in the GnomAD database, including 30,714 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 (18282 hom., cov: 33)
  • Exomes 𝑓: 0.50 (12432 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFMBT2	NM_001387889.1	c.1487+235T>C		intron_variant	Intron 13 of 20	ENST00000397167.6	NP_001374818.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFMBT2	ENST00000397167.6	c.1487+235T>C		intron_variant	Intron 13 of 20	5	NM_001387889.1	ENSP00000380353.1

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72682 AN: 151948 Hom.: 18277 Cov.: 33

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.474

GnomAD4 exome AF: 0.500 AC: 49165 AN: 98356 Hom.: 12432 Cov.: 0 AF XY: 0.501 AC XY: 22683 AN XY: 45320

African (AFR) AF: 0.331 AC: 765 AN: 2314

American (AMR) AF: 0.562 AC: 91 AN: 162

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 291 AN: 566

East Asian (EAS) AF: 0.831 AC: 399 AN: 480

South Asian (SAS) AF: 0.477 AC: 967 AN: 2028

European-Finnish (FIN) AF: 0.467 AC: 14 AN: 30

Middle Eastern (MID) AF: 0.397 AC: 73 AN: 184

European-Non Finnish (NFE) AF: 0.502 AC: 44911 AN: 89418

Other (OTH) AF: 0.521 AC: 1654 AN: 3174

GnomAD4 genome AF: 0.478 AC: 72723 AN: 152066 Hom.: 18282 Cov.: 33 AF XY: 0.481 AC XY: 35747 AN XY: 74348

African (AFR) AF: 0.360 AC: 14908 AN: 41468

American (AMR) AF: 0.536 AC: 8187 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1724 AN: 3472

East Asian (EAS) AF: 0.855 AC: 4411 AN: 5162

South Asian (SAS) AF: 0.505 AC: 2436 AN: 4822

European-Finnish (FIN) AF: 0.486 AC: 5133 AN: 10570

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.506 AC: 34374 AN: 67972

Other (OTH) AF: 0.473 AC: 1000 AN: 2114

Alfa AF: 0.486 Hom.: 34480

Bravo AF: 0.481

Asia WGS AF: 0.606 AC: 2106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.80
DANN	Benign	0.32
PhyloP100		-0.85
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: rs2147289; hg19: chr10-7244207;