rs1045634

Variant names:

• chr11-9778903-C-T
• rs1045634
• NM_030962.4:c.*1515G>A

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_030962.4(SBF2):​c.*1515G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 152,540 control chromosomes in the GnomAD database, including 9,206 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.33 (9160 hom., cov: 33)
  • Exomes 𝑓: 0.48 (46 hom.)
• Consequence: SBF2 NM_030962.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 1.32
• Publications: 8 publications found

Genes affected

SBF2 (HGNC:2135): (SET binding factor 2) This gene encodes a pseudophosphatase and member of the myotubularin-related protein family. This gene maps within the CMT4B2 candidate region of chromosome 11p15 and mutations in this gene have been associated with Charcot-Marie-Tooth Disease, type 4B2. [provided by RefSeq, Jul 2008]

SBF2-AS1 (HGNC:27438): (SBF2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BP6: Variant 11-9778903-C-T is Benign according to our data. Variant chr11-9778903-C-T is described in ClinVar as Benign. ClinVar VariationId is 306552.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030962.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SBF2	NM_030962.4	MANE Select	c.*1515G>A		3_prime_UTR	Exon 40 of 40	NP_112224.1	Q86WG5-1
	SBF2	NM_001386339.1		c.*1515G>A		3_prime_UTR	Exon 41 of 41	NP_001373268.1	A0A8I5KQ02
	SBF2	NM_001424318.1		c.*1515G>A		3_prime_UTR	Exon 41 of 41	NP_001411247.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SBF2	ENST00000256190.13	TSL:1 MANE Select	c.*1515G>A		3_prime_UTR	Exon 40 of 40	ENSP00000256190.8	Q86WG5-1
	SBF2	ENST00000689128.1		c.*1515G>A		3_prime_UTR	Exon 41 of 41	ENSP00000509587.1	A0A8I5KQ02
	SBF2	ENST00000675281.2		c.*1515G>A		3_prime_UTR	Exon 41 of 41	ENSP00000502491.1	A0A6Q8PH13

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50785 AN: 151986 Hom.: 9164 Cov.: 33

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.334

GnomAD4 exome AF: 0.479 AC: 208 AN: 434 Hom.: 46 Cov.: 0 AF XY: 0.465 AC XY: 121 AN XY: 260

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.481 AC: 205 AN: 426

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AF: 0.333 AC: 2 AN: 6

GnomAD4 genome AF: 0.334 AC: 50780 AN: 152106 Hom.: 9160 Cov.: 33 AF XY: 0.334 AC XY: 24805 AN XY: 74360

African (AFR) AF: 0.215 AC: 8926 AN: 41502

American (AMR) AF: 0.319 AC: 4872 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1281 AN: 3470

East Asian (EAS) AF: 0.319 AC: 1655 AN: 5186

South Asian (SAS) AF: 0.202 AC: 973 AN: 4818

European-Finnish (FIN) AF: 0.477 AC: 5043 AN: 10570

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26867 AN: 67978

Other (OTH) AF: 0.329 AC: 692 AN: 2106

Alfa AF: 0.369 Hom.: 18578

Bravo AF: 0.317

Asia WGS AF: 0.235 AC: 819 AN: 3474

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	1	Charcot-Marie-Tooth disease type 4B2 (1)
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	14
DANN	Benign	0.77
PhyloP100		1.3
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: rs1045634; hg19: chr11-9800450;