rs1330943

Variant names:

• chr13-89361193-A-G
• rs1330943
• ENST00000414049.1:n.2032T>C

Your query was ambiguous. Multiple possible variants found:

• chr13-89361193-A-G
• chr13-89361193-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414049.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SP3P	ENST00000414049.1	TSL:6	n.2032T>C		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.690 AC: 13368 AN: 19378

American (AMR) AF: 0.880 AC: 33843 AN: 38464

Ashkenazi Jewish (ASJ) AF: 0.989 AC: 17655 AN: 17856

East Asian (EAS) AF: 0.643 AC: 12572 AN: 19566

South Asian (SAS) AF: 0.943 AC: 71497 AN: 75816

European-Finnish (FIN) AF: 0.947 AC: 35608 AN: 37586

Middle Eastern (MID) AF: 0.964 AC: 3976 AN: 4126

European-Non Finnish (NFE) AF: 0.995 AC: 662472 AN: 665938

Other (OTH) AF: 0.953 AC: 35351 AN: 37084

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

African (AFR) AF: 0.661 AC: 27411 AN: 41442

American (AMR) AF: 0.910 AC: 13915 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.984 AC: 3413 AN: 3470

East Asian (EAS) AF: 0.625 AC: 3226 AN: 5160

South Asian (SAS) AF: 0.929 AC: 4475 AN: 4818

European-Finnish (FIN) AF: 0.936 AC: 9837 AN: 10512

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.991 AC: 67418 AN: 68034

Other (OTH) AF: 0.900 AC: 1899 AN: 2110

Alfa AF: 0.915 Hom.: 9537

Bravo AF: 0.861

Asia WGS AF: 0.770 AC: 2678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	10
DANN	Benign	0.41
PhyloP100		3.9

Splicing

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

Other links and lift over

dbSNP: rs1330943; hg19: chr13-90013447;