12-53338107-G-A

Position:

• chr12-53338107-G-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001300837.2(SP7):​c.-271-1724C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.71 (25459 hom., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: SP7 NM_001300837.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

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 -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SP7	NM_001300837.2	c.-271-1724C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SP7	ENST00000547755.1	c.-34+7007C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 83739 AN: 118426 Hom.: 25449 Cov.: 20 FAILED QC

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.939

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.735

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.704

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.707 AC: 83785 AN: 118500 Hom.: 25459 Cov.: 20 AF XY: 0.716 AC XY: 41375 AN XY: 57816

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.763

Gnomad4 ASJ AF: 0.733

Gnomad4 EAS AF: 0.938

Gnomad4 SAS AF: 0.855

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.707

Alfa AF: 0.718 Hom.: 85890

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.7
DANN	Benign	0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10876432; hg19: chr12-53731891;