rs1330943

chr13-89361193-A-Gchr13-89361193-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000414049.1(SP3P):n.2032T>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.954 in 1,067,862 control chromosomes in the GnomAD database, including 490,978 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 0.87 (59655 hom., cov: 32)
  • Exomes 𝑓: 0.97 (431323 hom.)
• Consequence: SP3P ENST00000414049.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.85

Genes affected

SP3P (HGNC:35430): (Sp3 transcription factor pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.985 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SP3P	ENST00000414049.1	n.2032T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.874 AC: 132723 AN: 151930 Hom.: 59637 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.929

Gnomad FIN AF: 0.936

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.991

Gnomad OTH AF: 0.902

GnomAD4 exome AF: 0.968 AC: 886342 AN: 915814 Hom.: 431323 Cov.: 13 AF XY: 0.968 AC XY: 455897 AN XY: 470868

Gnomad4 AFR exome AF: 0.690

Gnomad4 AMR exome AF: 0.880

Gnomad4 ASJ exome AF: 0.989

Gnomad4 EAS exome AF: 0.643

Gnomad4 SAS exome AF: 0.943

Gnomad4 FIN exome AF: 0.947

Gnomad4 NFE exome AF: 0.995

Gnomad4 OTH exome AF: 0.953

GnomAD4 genome AF: 0.873 AC: 132790 AN: 152048 Hom.: 59655 Cov.: 32 AF XY: 0.870 AC XY: 64670 AN XY: 74312

Gnomad4 AFR AF: 0.661

Gnomad4 AMR AF: 0.910

Gnomad4 ASJ AF: 0.984

Gnomad4 EAS AF: 0.625

Gnomad4 SAS AF: 0.929

Gnomad4 FIN AF: 0.936

Gnomad4 NFE AF: 0.991

Gnomad4 OTH AF: 0.900

Alfa AF: 0.925 Hom.: 9377

Bravo AF: 0.861

Asia WGS AF: 0.770 AC: 2678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
Cadd	Benign	10
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1330943; hg19: chr13-90013447;