chr9-38478673-A-T

Variant names:

• chr9-38478673-A-T
• rs2799738
• ENST00000443005.1:n.203A>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

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

ENSG00000291061 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000443005.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCEA1P3	ENST00000443005.1	TSL:6	n.203A>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000291061	ENST00000635962.1	TSL:5	n.1044+6740A>T		intron	N/A
	ENSG00000291061	ENST00000685989.1		n.1044+6740A>T		intron	N/A

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

African (AFR) AF: 0.250 AC: 3 AN: 12

American (AMR) AF: 0.500 AC: 8 AN: 16

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 6 AN: 20

East Asian (EAS) AF: 0.00 AC: 0 AN: 10

South Asian (SAS) AF: 0.333 AC: 44 AN: 132

European-Finnish (FIN) AF: 0.184 AC: 297 AN: 1610

Middle Eastern (MID) AF: 0.667 AC: 4 AN: 6

European-Non Finnish (NFE) AF: 0.270 AC: 303 AN: 1124

Other (OTH) AF: 0.254 AC: 31 AN: 122

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

African (AFR) AF: 0.384 AC: 15907 AN: 41474

American (AMR) AF: 0.296 AC: 4521 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1267 AN: 3468

East Asian (EAS) AF: 0.186 AC: 962 AN: 5172

South Asian (SAS) AF: 0.278 AC: 1343 AN: 4826

European-Finnish (FIN) AF: 0.213 AC: 2254 AN: 10580

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20842 AN: 68002

Other (OTH) AF: 0.326 AC: 690 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	5.1
DANN	Benign	0.56
PhyloP100		6.4

Splicing

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

Other links and lift over

dbSNP: rs2799738; hg19: chr9-38478670;