rs2799738

Positions:

• chr9-38478673-A-T

Variant summary

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

The ENST00000443005.1(TCEA1P3):​n.203A>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.315 in 155,190 control chromosomes in the GnomAD database, including 7,984 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 0.32 (7889 hom., cov: 32)
  • Exomes 𝑓: 0.23 (95 hom.)
• Consequence: TCEA1P3 ENST00000443005.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.44

Genes affected

TCEA1P3 (HGNC:30569): (transcription elongation factor A1 pseudogene 3)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TCEA1P3	ENST00000443005.1	n.203A>T		non_coding_transcript_exon_variant	1/1
	ENST00000635962.1	n.1044+6740A>T		intron_variant, non_coding_transcript_variant		5
	ENST00000685989.1	n.1044+6740A>T		intron_variant, non_coding_transcript_variant
	ENST00000701648.1	n.446+6740A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48180 AN: 152020 Hom.: 7877 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.329

GnomAD4 exome AF: 0.228 AC: 696 AN: 3052 Hom.: 95 Cov.: 0 AF XY: 0.230 AC XY: 372 AN XY: 1616

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.300

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.333

Gnomad4 FIN exome AF: 0.184

Gnomad4 NFE exome AF: 0.270

Gnomad4 OTH exome AF: 0.254

GnomAD4 genome AF: 0.317 AC: 48228 AN: 152138 Hom.: 7889 Cov.: 32 AF XY: 0.311 AC XY: 23095 AN XY: 74366

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.326

Alfa AF: 0.317 Hom.: 950

Bravo AF: 0.325

Asia WGS AF: 0.247 AC: 857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	5.1
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2799738; hg19: chr9-38478670;