rs3829252

Variant names:

• chr11-9779904-G-A
• rs3829252
• NM_030962.4:c.*514C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-9779904-G-A
• chr11-9779904-G-C
• chr11-9779904-G-T

Variant summary

Our verdict is Benign. The variant received -18 ACMG points: 0P and 18B. BP4_Moderate BP6_Very_Strong BA1

The NM_030962.4(SBF2):​c.*514C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 203,806 control chromosomes in the GnomAD database, including 12,476 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.33 (9200 hom., cov: 32)
  • Exomes 𝑓: 0.34 (3276 hom.)
• Consequence: SBF2 NM_030962.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 1.26
• Publications: 10 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 -18 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BP6: Variant 11-9779904-G-A is Benign according to our data. Variant chr11-9779904-G-A is described in ClinVar as Benign. ClinVar VariationId is 306564.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.*514C>T		3_prime_UTR	Exon 40 of 40	NP_112224.1	Q86WG5-1
	SBF2	NM_001386339.1		c.*514C>T		3_prime_UTR	Exon 41 of 41	NP_001373268.1	A0A8I5KQ02
	SBF2	NM_001424318.1		c.*514C>T		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.*514C>T		3_prime_UTR	Exon 40 of 40	ENSP00000256190.8	Q86WG5-1
	SBF2	ENST00000689128.1		c.*514C>T		3_prime_UTR	Exon 41 of 41	ENSP00000509587.1	A0A8I5KQ02
	SBF2	ENST00000675281.2		c.*514C>T		3_prime_UTR	Exon 41 of 41	ENSP00000502491.1	A0A6Q8PH13

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50894 AN: 151912 Hom.: 9204 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.334

GnomAD4 exome AF: 0.336 AC: 17416 AN: 51776 Hom.: 3276 Cov.: 0 AF XY: 0.326 AC XY: 8814 AN XY: 27008

African (AFR) AF: 0.180 AC: 420 AN: 2328

American (AMR) AF: 0.297 AC: 1155 AN: 3886

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 392 AN: 1106

East Asian (EAS) AF: 0.329 AC: 1377 AN: 4184

South Asian (SAS) AF: 0.201 AC: 1194 AN: 5954

European-Finnish (FIN) AF: 0.432 AC: 825 AN: 1910

Middle Eastern (MID) AF: 0.309 AC: 50 AN: 162

European-Non Finnish (NFE) AF: 0.374 AC: 11125 AN: 29772

Other (OTH) AF: 0.355 AC: 878 AN: 2474

GnomAD4 genome AF: 0.335 AC: 50889 AN: 152030 Hom.: 9200 Cov.: 32 AF XY: 0.334 AC XY: 24841 AN XY: 74276

African (AFR) AF: 0.217 AC: 9019 AN: 41468

American (AMR) AF: 0.320 AC: 4889 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1289 AN: 3470

East Asian (EAS) AF: 0.321 AC: 1657 AN: 5168

South Asian (SAS) AF: 0.202 AC: 975 AN: 4818

European-Finnish (FIN) AF: 0.476 AC: 5019 AN: 10536

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26872 AN: 67978

Other (OTH) AF: 0.328 AC: 693 AN: 2114

Alfa AF: 0.366 Hom.: 13182

Bravo AF: 0.318

Asia WGS AF: 0.238 AC: 829 AN: 3478

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	-0.46
CADD	Benign	15
DANN	Benign	0.74
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: rs3829252; hg19: chr11-9801451;