13-40911532-T-G

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000632487.1(SUGT1P3):​n.162-3320A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: SUGT1P3 ENST00000632487.1 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TPTE2P5	NR_038258.1	n.132+10087A>C		intron_variant	Intron 1 of 7
TPTE2P5	NR_038259.1	n.132+10087A>C		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUGT1P3	ENST00000379515.4	n.131+10087A>C		intron_variant	Intron 1 of 5	5
SUGT1P3	ENST00000432905.6	n.171+10087A>C		intron_variant	Intron 1 of 4	5
SUGT1P3	ENST00000604259.5	n.329+202A>C		intron_variant	Intron 5 of 5	6

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.3
DANN	Benign	0.72
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;