chr10-7188562-G-T

Variant names:

• chr10-7188562-G-T
• rs2462712
• NM_001387889.1:c.1808+62C>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.1808+62C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 1,360,230 control chromosomes in the GnomAD database, including 256,565 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 0.61 (29454 hom., cov: 32)
  • Exomes 𝑓: 0.61 (227111 hom.)
• Consequence: SFMBT2 NM_001387889.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 7 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 (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFMBT2	NM_001387889.1	c.1808+62C>A		intron_variant	Intron 16 of 20	ENST00000397167.6	NP_001374818.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFMBT2	ENST00000397167.6	c.1808+62C>A		intron_variant	Intron 16 of 20	5	NM_001387889.1	ENSP00000380353.1

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93399 AN: 151922 Hom.: 29421 Cov.: 32

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.622

GnomAD4 exome AF: 0.607 AC: 732871 AN: 1208190 Hom.: 227111 AF XY: 0.605 AC XY: 368710 AN XY: 609834

African (AFR) AF: 0.669 AC: 18929 AN: 28288

American (AMR) AF: 0.501 AC: 20464 AN: 40856

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 13449 AN: 23172

East Asian (EAS) AF: 0.169 AC: 6460 AN: 38230

South Asian (SAS) AF: 0.576 AC: 44503 AN: 77222

European-Finnish (FIN) AF: 0.628 AC: 31818 AN: 50690

Middle Eastern (MID) AF: 0.619 AC: 3030 AN: 4898

European-Non Finnish (NFE) AF: 0.631 AC: 563251 AN: 892960

Other (OTH) AF: 0.597 AC: 30967 AN: 51874

GnomAD4 genome AF: 0.615 AC: 93480 AN: 152040 Hom.: 29454 Cov.: 32 AF XY: 0.611 AC XY: 45436 AN XY: 74304

African (AFR) AF: 0.669 AC: 27729 AN: 41456

American (AMR) AF: 0.580 AC: 8865 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2026 AN: 3472

East Asian (EAS) AF: 0.181 AC: 936 AN: 5174

South Asian (SAS) AF: 0.560 AC: 2694 AN: 4814

European-Finnish (FIN) AF: 0.632 AC: 6662 AN: 10544

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.623 AC: 42358 AN: 67988

Other (OTH) AF: 0.623 AC: 1311 AN: 2106

Alfa AF: 0.618 Hom.: 46937

Bravo AF: 0.609

Asia WGS AF: 0.423 AC: 1471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.45
PhyloP100		0.077
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: rs2462712; hg19: chr10-7230524; COSMIC: COSV62806884;