chr13-40911532-T-C

Variant names:

• chr13-40911532-T-C
• rs1989252
• ENST00000379515.4:n.131+10087A>G

Variant summary

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

The ENST00000379515.4(SUGT1P3):​n.131+10087A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 151,992 control chromosomes in the GnomAD database, including 9,393 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 0.34 (9393 hom., cov: 32)
• Consequence: SUGT1P3 ENST00000379515.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135
• Publications: 12 publications found

Genes affected

SUGT1P3 (HGNC:):

SUGT1P3 (HGNC:20513): (SUGT1 pseudogene 3)

TPTE2P5 (HGNC:42356): (TPTE2 pseudogene 5)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000379515.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TPTE2P5	NR_038258.1		n.132+10087A>G		intron	N/A
	TPTE2P5	NR_038259.1		n.132+10087A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUGT1P3	ENST00000379515.4	TSL:5	n.131+10087A>G		intron	N/A
	SUGT1P3	ENST00000432905.6	TSL:5	n.171+10087A>G		intron	N/A
	SUGT1P3	ENST00000604259.5	TSL:6	n.329+202A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51547 AN: 151874 Hom.: 9373 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.340 AC: 51615 AN: 151992 Hom.: 9393 Cov.: 32 AF XY: 0.339 AC XY: 25194 AN XY: 74290

African (AFR) AF: 0.383 AC: 15873 AN: 41446

American (AMR) AF: 0.280 AC: 4280 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1050 AN: 3468

East Asian (EAS) AF: 0.756 AC: 3907 AN: 5166

South Asian (SAS) AF: 0.366 AC: 1766 AN: 4826

European-Finnish (FIN) AF: 0.285 AC: 3012 AN: 10568

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.306 AC: 20771 AN: 67920

Other (OTH) AF: 0.326 AC: 688 AN: 2112

Alfa AF: 0.317 Hom.: 2144

Bravo AF: 0.339

Asia WGS AF: 0.555 AC: 1921 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.6
DANN	Benign	0.78
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1989252; hg19: chr13-41485668;