3-52931239-C-T

Variant names:

• chr3-52931239-C-T
• rs10510761
• NM_016329.4:c.701-204G>A

Variant summary

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

The NM_016329.4(SFMBT1):​c.701-204G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.092 in 152,138 control chromosomes in the GnomAD database, including 668 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 0.092 (668 hom., cov: 32)
• Consequence: SFMBT1 NM_016329.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.671
• Publications: 10 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFMBT1	NM_016329.4	c.701-204G>A		intron_variant	Intron 6 of 20	ENST00000394752.8	NP_057413.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFMBT1	ENST00000394752.8	c.701-204G>A		intron_variant	Intron 6 of 20	1	NM_016329.4	ENSP00000378235.2

Frequencies

GnomAD3 genomes AF: 0.0920 AC: 13982 AN: 152020 Hom.: 665 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.0965

Gnomad ASJ AF: 0.0856

Gnomad EAS AF: 0.0574

Gnomad SAS AF: 0.0587

Gnomad FIN AF: 0.0518

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0949

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0920 AC: 14003 AN: 152138 Hom.: 668 Cov.: 32 AF XY: 0.0882 AC XY: 6563 AN XY: 74384

African (AFR) AF: 0.104 AC: 4328 AN: 41496

American (AMR) AF: 0.0963 AC: 1470 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0856 AC: 297 AN: 3468

East Asian (EAS) AF: 0.0577 AC: 299 AN: 5180

South Asian (SAS) AF: 0.0590 AC: 284 AN: 4816

European-Finnish (FIN) AF: 0.0518 AC: 548 AN: 10576

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0949 AC: 6455 AN: 68014

Other (OTH) AF: 0.103 AC: 218 AN: 2112

Alfa AF: 0.0877 Hom.: 125

Bravo AF: 0.0966

Asia WGS AF: 0.0760 AC: 263 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.67
DANN	Benign	0.51
PhyloP100		-0.67
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: rs10510761; hg19: chr3-52965255;