3-53028645-T-C

Variant names:

• chr3-53028645-T-C
• rs9847710
• NM_016329.4:c.-131+17171A>G

Variant summary

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

The NM_016329.4(SFMBT1):​c.-131+17171A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 151,764 control chromosomes in the GnomAD database, including 16,490 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 0.46 (16490 hom., cov: 31)
• Consequence: SFMBT1 NM_016329.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379
• Publications: 56 publications found

Genes affected

SFMBT1 (HGNC:20255): (Scm like with four mbt domains 1) This gene shares high similarity with the Drosophila Scm (sex comb on midleg) gene. It encodes a protein which contains four malignant brain tumor repeat (mbt) domains and may be involved in antigen recognition. [provided by RefSeq, Jun 2012]

ENSG00000272305 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016329.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFMBT1	NM_016329.4	MANE Select	c.-131+17171A>G		intron	N/A	NP_057413.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFMBT1	ENST00000394752.8	TSL:1 MANE Select	c.-131+17171A>G		intron	N/A	ENSP00000378235.2
	ENSG00000272305	ENST00000607283.5	TSL:5	n.*213-9523A>G		intron	N/A	ENSP00000475819.1
	SFMBT1	ENST00000482396.5	TSL:2	c.-131+14491A>G		intron	N/A	ENSP00000418860.1

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69778 AN: 151646 Hom.: 16459 Cov.: 31

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.465

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.460 AC: 69864 AN: 151764 Hom.: 16490 Cov.: 31 AF XY: 0.463 AC XY: 34330 AN XY: 74142

African (AFR) AF: 0.516 AC: 21338 AN: 41346

American (AMR) AF: 0.467 AC: 7124 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1410 AN: 3466

East Asian (EAS) AF: 0.625 AC: 3210 AN: 5136

South Asian (SAS) AF: 0.629 AC: 3025 AN: 4808

European-Finnish (FIN) AF: 0.386 AC: 4064 AN: 10522

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28209 AN: 67918

Other (OTH) AF: 0.465 AC: 980 AN: 2106

Alfa AF: 0.431 Hom.: 62135

Bravo AF: 0.467

Asia WGS AF: 0.612 AC: 2129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.68
PhyloP100		-0.38
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: rs9847710; hg19: chr3-53062661;