chr13-24959693-A-C

Variant names:

• chr13-24959693-A-C
• rs2483374
• ENST00000429698.3:n.297-8205T>G

Variant summary

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

The ENST00000429698.3(ENSG00000291041):​n.297-8205T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 412,964 control chromosomes in the GnomAD database, including 51,974 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 0.49 (19143 hom., cov: 32)
  • Exomes 𝑓: 0.50 (32831 hom.)
• Consequence: ENSG00000291041 ENST00000429698.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.664
• Publications: 5 publications found

Genes affected

ENSG00000291041 (HGNC:):

TPTE2P1 (HGNC:35196): (TPTE2 pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000429698.3. 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
	TPTE2P1	NR_026730.2		n.280-8205T>G		intron	N/A
	TPTE2P1	NR_178209.1		n.280-8205T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291041	ENST00000429698.3	TSL:3	n.297-8205T>G		intron	N/A
	ENSG00000291041	ENST00000434100.5	TSL:3	n.134+7699T>G		intron	N/A
	TPTE2P1	ENST00000435256.1	TSL:6	n.329+41T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74998 AN: 151844 Hom.: 19120 Cov.: 32

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.506

GnomAD4 exome AF: 0.496 AC: 129559 AN: 261002 Hom.: 32831 Cov.: 5 AF XY: 0.502 AC XY: 68911 AN XY: 137346

African (AFR) AF: 0.601 AC: 3194 AN: 5312

American (AMR) AF: 0.384 AC: 1812 AN: 4716

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 2547 AN: 4812

East Asian (EAS) AF: 0.304 AC: 1748 AN: 5758

South Asian (SAS) AF: 0.574 AC: 8359 AN: 14566

European-Finnish (FIN) AF: 0.374 AC: 8206 AN: 21960

Middle Eastern (MID) AF: 0.571 AC: 474 AN: 830

European-Non Finnish (NFE) AF: 0.509 AC: 97469 AN: 191668

Other (OTH) AF: 0.505 AC: 5750 AN: 11380

GnomAD4 genome AF: 0.494 AC: 75058 AN: 151962 Hom.: 19143 Cov.: 32 AF XY: 0.488 AC XY: 36274 AN XY: 74272

African (AFR) AF: 0.592 AC: 24503 AN: 41418

American (AMR) AF: 0.420 AC: 6414 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1739 AN: 3470

East Asian (EAS) AF: 0.278 AC: 1427 AN: 5138

South Asian (SAS) AF: 0.530 AC: 2555 AN: 4820

European-Finnish (FIN) AF: 0.368 AC: 3884 AN: 10568

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32665 AN: 67962

Other (OTH) AF: 0.510 AC: 1079 AN: 2116

Alfa AF: 0.485 Hom.: 48951

Bravo AF: 0.499

Asia WGS AF: 0.445 AC: 1550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.1
DANN	Benign	0.35
PhyloP100		-0.66

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2483374;

hg19: chr13-25533831;