chr3-53028645-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFMBT1	NM_016329.4	c.-131+17171A>G		intron_variant	Intron 1 of 20	ENST00000394752.8	NP_057413.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFMBT1	ENST00000394752.8	c.-131+17171A>G		intron_variant	Intron 1 of 20	1	NM_016329.4	ENSP00000378235.2
ENSG00000272305	ENST00000607283.5	n.*213-9523A>G		intron_variant	Intron 4 of 4	5		ENSP00000475819.1

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

Gnomad4 AFR AF: 0.516

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.625

Gnomad4 SAS AF: 0.629

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.465

Alfa AF: 0.429 Hom.: 28908

Bravo AF: 0.467

Asia WGS AF: 0.612 AC: 2129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.68

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

Publications

LitVar

Other links and lift over

dbSNP: rs9847710; hg19: chr3-53062661;