10-7277326-C-A

Variant names:

• chr10-7277326-C-A
• rs7080643
• NM_001387889.1:c.773-337G>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.773-337G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 214,282 control chromosomes in the GnomAD database, including 43,056 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 0.65 (34207 hom., cov: 31)
  • Exomes 𝑓: 0.53 (8849 hom.)
• Consequence: SFMBT2 NM_001387889.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFMBT2	NM_001387889.1	c.773-337G>T		intron_variant	Intron 6 of 20	ENST00000397167.6	NP_001374818.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFMBT2	ENST00000397167.6	c.773-337G>T		intron_variant	Intron 6 of 20	5	NM_001387889.1	ENSP00000380353.1

Frequencies

GnomAD3 genomes AF: 0.652 AC: 98857 AN: 151638 Hom.: 34148 Cov.: 31

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.591

GnomAD4 exome AF: 0.526 AC: 32903 AN: 62524 Hom.: 8849 AF XY: 0.524 AC XY: 15316 AN XY: 29238

African (AFR) AF: 0.903 AC: 1300 AN: 1440

American (AMR) AF: 0.604 AC: 64 AN: 106

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 184 AN: 346

East Asian (EAS) AF: 0.770 AC: 228 AN: 296

South Asian (SAS) AF: 0.363 AC: 479 AN: 1318

European-Finnish (FIN) AF: 0.550 AC: 11 AN: 20

Middle Eastern (MID) AF: 0.398 AC: 47 AN: 118

European-Non Finnish (NFE) AF: 0.519 AC: 29541 AN: 56922

Other (OTH) AF: 0.536 AC: 1049 AN: 1958

GnomAD4 genome AF: 0.652 AC: 98972 AN: 151758 Hom.: 34207 Cov.: 31 AF XY: 0.653 AC XY: 48435 AN XY: 74166

African (AFR) AF: 0.884 AC: 36672 AN: 41490

American (AMR) AF: 0.693 AC: 10591 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1820 AN: 3454

East Asian (EAS) AF: 0.777 AC: 4018 AN: 5168

South Asian (SAS) AF: 0.404 AC: 1911 AN: 4734

European-Finnish (FIN) AF: 0.633 AC: 6639 AN: 10494

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.523 AC: 35478 AN: 67838

Other (OTH) AF: 0.587 AC: 1236 AN: 2106

Alfa AF: 0.520 Hom.: 4104

Bravo AF: 0.673

Asia WGS AF: 0.574 AC: 1998 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	0.018
DANN	Benign	0.56
PhyloP100		-0.37
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: rs7080643; hg19: chr10-7319288;