rs372961085

Variant names:

• chr12-53328227-C-G
• NM_001173467.3:c.1215G>C

Your query was ambiguous. Multiple possible variants found:

• chr12-53328227-C-G
• chr12-53328227-C-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001173467.3(SP7):​c.1215G>C​(p.Thr405Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. T405T) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SP7 NM_001173467.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44

Genes affected

SP7 (HGNC:17321): (Sp7 transcription factor) This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein is a bone specific transcription factor and is required for osteoblast differentiation and bone formation.[provided by RefSeq, Jul 2010]

ACMG classification

Verdict is Likely_benign. Variant got -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP7: Synonymous conserved (PhyloP=-2.44 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SP7	NM_001173467.3	c.1215G>C	p.Thr405Thr	synonymous_variant	Exon 3 of 3	ENST00000536324.4	NP_001166938.1
SP7	NM_152860.2	c.1215G>C	p.Thr405Thr	synonymous_variant	Exon 2 of 2		NP_690599.1
SP7	NM_001300837.2	c.1161G>C	p.Thr387Thr	synonymous_variant	Exon 3 of 3		NP_001287766.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SP7	ENST00000536324.4	c.1215G>C	p.Thr405Thr	synonymous_variant	Exon 3 of 3	2	NM_001173467.3	ENSP00000443827.2
SP7	ENST00000303846.3	c.1215G>C	p.Thr405Thr	synonymous_variant	Exon 2 of 2	1		ENSP00000302812.3
SP7	ENST00000537210.2	c.1161G>C	p.Thr387Thr	synonymous_variant	Exon 2 of 2	1		ENSP00000441367.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.10
DANN	Benign	0.60

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr12-53722011;