rs5944858

chrX-102127445-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6 BP7 BA1

The NM_080390.4(TCEAL2):c.615G>A(p.Arg205=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 1,199,996 control chromosomes in the GnomAD database, including 10,478 homozygotes. There are 58,806 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.12 (820 hom., 3668 hem., cov: 23)
  • Exomes 𝑓: 0.16 (9658 hom. 55138 hem.)
• Consequence: TCEAL2 NM_080390.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.742

Genes affected

TCEAL2 (HGNC:29818): (transcription elongation factor A like 2) This gene encodes a member of the transcription elongation factor A (SII)-like (TCEAL) gene family. Members of this family contain TFA domains and may function as nuclear phosphoproteins that modulate transcription in a promoter context-dependent manner. Multiple family members are located on the X chromosome. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BP6: Variant X-102127445-G-A is Benign according to our data. Variant chrX-102127445-G-A is described in Lovd as [Likely_benign].
• BP7: Synonymous conserved (PhyloP=0.742 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TCEAL2	NM_080390.4	c.615G>A	p.Arg205=	synonymous_variant	3/3	ENST00000372780.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TCEAL2	ENST00000372780.6	c.615G>A	p.Arg205=	synonymous_variant	3/3	1	NM_080390.4	P1
TCEAL2	ENST00000329035.2	c.615G>A	p.Arg205=	synonymous_variant	3/3	5		P1
TCEAL2	ENST00000651085.1	n.153+1000G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.119 AC: 13251 AN: 110898 Hom.: 820 Cov.: 23 AF XY: 0.111 AC XY: 3669 AN XY: 33128

Gnomad AFR AF: 0.0313

Gnomad AMI AF: 0.0498

Gnomad AMR AF: 0.0971

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.00225

Gnomad SAS AF: 0.0357

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.157

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.118

GnomAD3 exomes AF: 0.0907 AC: 14545 AN: 160391 Hom.: 896 AF XY: 0.0858 AC XY: 4701 AN XY: 54761

Gnomad AFR exome AF: 0.0199

Gnomad AMR exome AF: 0.0464

Gnomad ASJ exome AF: 0.0983

Gnomad EAS exome AF: 0.000902

Gnomad SAS exome AF: 0.0288

Gnomad FIN exome AF: 0.177

Gnomad NFE exome AF: 0.129

Gnomad OTH exome AF: 0.114

GnomAD4 exome AF: 0.156 AC: 169580 AN: 1089045 Hom.: 9658 Cov.: 32 AF XY: 0.155 AC XY: 55138 AN XY: 356127

Gnomad4 AFR exome AF: 0.0265

Gnomad4 AMR exome AF: 0.0678

Gnomad4 ASJ exome AF: 0.153

Gnomad4 EAS exome AF: 0.000331

Gnomad4 SAS exome AF: 0.0499

Gnomad4 FIN exome AF: 0.202

Gnomad4 NFE exome AF: 0.174

Gnomad4 OTH exome AF: 0.143

GnomAD4 genome AF: 0.119 AC: 13248 AN: 110951 Hom.: 820 Cov.: 23 AF XY: 0.111 AC XY: 3668 AN XY: 33191

Gnomad4 AFR AF: 0.0312

Gnomad4 AMR AF: 0.0969

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.00226

Gnomad4 SAS AF: 0.0358

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.116

Alfa AF: 0.148 Hom.: 1278

Bravo AF: 0.112

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	7.7
Dann	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs5944858; hg19: chrX-101382417;