rs9532645

Variant names:

• chr13-40880898-G-A
• rs9532645
• ENST00000633814.2:n.2300C>T

Your query was ambiguous. Multiple possible variants found:

• chr13-40880898-G-A
• chr13-40880898-G-C

Variant summary

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

The ENST00000633814.2(SUGT1P3):​n.2300C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 152,082 control chromosomes in the GnomAD database, including 25,325 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 0.54 (25325 hom., cov: 32)
• Consequence: SUGT1P3 ENST00000633814.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 3 publications found

Genes affected

SUGT1P3 (HGNC:):

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TPTE2P5	NR_038258.1	n.133-25083C>T		intron_variant	Intron 1 of 7
TPTE2P5	NR_038259.1	n.133-25083C>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUGT1P3	ENST00000633814.2	n.2300C>T		non_coding_transcript_exon_variant	Exon 3 of 3	3
SUGT1P3	ENST00000842400.1	n.364C>T		non_coding_transcript_exon_variant	Exon 3 of 3
SUGT1P3	ENST00000379515.4	n.132-25083C>T		intron_variant	Intron 1 of 5	5

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81504 AN: 151964 Hom.: 25337 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.536 AC: 81498 AN: 152082 Hom.: 25325 Cov.: 32 AF XY: 0.541 AC XY: 40211 AN XY: 74354

African (AFR) AF: 0.229 AC: 9501 AN: 41472

American (AMR) AF: 0.653 AC: 9990 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2251 AN: 3472

East Asian (EAS) AF: 0.174 AC: 901 AN: 5180

South Asian (SAS) AF: 0.584 AC: 2814 AN: 4820

European-Finnish (FIN) AF: 0.713 AC: 7543 AN: 10580

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.683 AC: 46399 AN: 67964

Other (OTH) AF: 0.565 AC: 1187 AN: 2100

Alfa AF: 0.625 Hom.: 52785

Bravo AF: 0.520

Asia WGS AF: 0.348 AC: 1210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.79
DANN	Benign	0.47
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs9532645; hg19: chr13-41455034; COSMIC: COSV65346936;