chr13-40911532-T-C

Position:

• chr13-40911532-T-C

Variant summary

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

The ENST00000632487.1(SUGT1P3):​n.162-3320A>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 ENST00000632487.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

Genes affected

ENSG00000290476 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TPTE2P5	NR_038258.1	n.132+10087A>G		intron_variant
TPTE2P5	NR_038259.1	n.132+10087A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000290476	ENST00000379515.3	n.131+10087A>G		intron_variant		5
SUGT1P3	ENST00000604259.5	n.329+202A>G		intron_variant		6
SUGT1P3	ENST00000632487.1	n.162-3320A>G		intron_variant		2

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

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.280

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.326

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1989252; hg19: chr13-41485668;