X-103330974-G-A

Variant names:

• chrX-103330974-G-A
• rs1045761
• NM_152278.5:c.-94G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001348258.2(TCEAL7):​c.-91-3G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 22)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: TCEAL7 NM_001348258.2 splice_region, intron
• Scores: Splicing: ADA: 0.0002553
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363
• Publications: 7 publications found

Genes affected

TCEAL7 (HGNC:28336): (transcription elongation factor A like 7) Predicted to enable WW domain binding activity. Involved in negative regulation of NF-kappaB transcription factor activity and negative regulation of transcription, DNA-templated. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001348258.2. 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
	TCEAL7	NM_152278.5	MANE Select	c.-94G>A		5_prime_UTR	Exon 2 of 3	NP_689491.1	Q9BRU2
	TCEAL7	NM_001348258.2		c.-91-3G>A		splice_region intron	N/A	NP_001335187.1	Q9BRU2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCEAL7	ENST00000332431.5	TSL:1 MANE Select	c.-94G>A		5_prime_UTR	Exon 2 of 3	ENSP00000329794.4	Q9BRU2
	TCEAL7	ENST00000861133.1		c.-94G>A		5_prime_UTR	Exon 1 of 2	ENSP00000531192.1
	TCEAL7	ENST00000932017.1		c.-92G>A		5_prime_UTR	Exon 2 of 3	ENSP00000602076.1

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 3599 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 833

African (AFR) AF: 0.00 AC: 0 AN: 103

American (AMR) AF: 0.00 AC: 0 AN: 262

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 89

East Asian (EAS) AF: 0.00 AC: 0 AN: 113

South Asian (SAS) AF: 0.00 AC: 0 AN: 101

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 377

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2370

Other (OTH) AF: 0.00 AC: 0 AN: 179

GnomAD4 genome Cov.: 22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.63
PhyloP100		0.36

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00026
dbscSNV1_RF	Benign	0.038
SpliceAI score (max)		0.23		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.23		Position offset: 3

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

Other links and lift over

dbSNP: rs1045761; hg19: chrX-102585902;