chrX-103609637-G-A

Variant names:

• chrX-103609637-G-A
• rs74490974
• NM_032926.3:c.573G>A

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_Strong BP7

The NM_032926.3(TCEAL3):​c.573G>A​(p.Gln191Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. 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 0.0000090 (0 hom., 1 hem., cov: 23)
  • Exomes 𝑓: 0.00017 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: TCEAL3 NM_032926.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500

Genes affected

TCEAL3 (HGNC:28247): (transcription elongation factor A like 3) 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. Alternative splicing results in multiple transcript variants encoding a single isoform. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BP7: Synonymous conserved (PhyloP=-0.05 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCEAL3	NM_032926.3	c.573G>A	p.Gln191Gln	synonymous_variant	Exon 3 of 3	ENST00000372627.10	NP_116315.1
TCEAL3	NM_001006933.2	c.573G>A	p.Gln191Gln	synonymous_variant	Exon 3 of 3		NP_001006934.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCEAL3	ENST00000372627.10	c.573G>A	p.Gln191Gln	synonymous_variant	Exon 3 of 3	1	NM_032926.3	ENSP00000361710.5
TCEAL3	ENST00000243286.7	c.573G>A	p.Gln191Gln	synonymous_variant	Exon 3 of 3	1		ENSP00000243286.3
TCEAL3	ENST00000372628.5	c.573G>A	p.Gln191Gln	synonymous_variant	Exon 3 of 3	5		ENSP00000361711.1
TCEAL3	ENST00000477014.1	n.159-874G>A		intron_variant	Intron 2 of 6	5

Frequencies

GnomAD3 genomes AF: 0.00000896 AC: 1 AN: 111613 Hom.: 0 Cov.: 23 AF XY: 0.0000296 AC XY: 1 AN XY: 33799

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000189

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000165 AC: 145 AN: 876195 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 275081

Gnomad4 AFR exome AF: 0.000229

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.000120

Gnomad4 EAS exome AF: 0.0000706

Gnomad4 SAS exome AF: 0.0000863

Gnomad4 FIN exome AF: 0.0000815

Gnomad4 NFE exome AF: 0.000195

Gnomad4 OTH exome AF: 0.0000518

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000896 AC: 1 AN: 111613 Hom.: 0 Cov.: 23 AF XY: 0.0000296 AC XY: 1 AN XY: 33799

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000189

Gnomad4 OTH AF: 0.00

Alfa AF: 0.185 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	2.0
DANN	Benign	0.64

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: rs74490974; hg19: chrX-102864565; COSMIC: COSV54580262;