rs917472096

Variant names:

• chrX-80022375-C-A
• rs917472096
• NM_001109878.2:c.106C>A

Your query was ambiguous. Multiple possible variants found:

• chrX-80022375-C-A
• chrX-80022375-C-G
• chrX-80022375-C-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001109878.2(TBX22):​c.106C>A​(p.Arg36Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000365 in 1,096,427 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. 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: not found (cov: 22)
  • Exomes 𝑓: 0.0000036 (0 hom. 1 hem.)
• Consequence: TBX22 NM_001109878.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

Genes affected

TBX22 (HGNC:11600): (T-box transcription factor 22) This gene is a member of a phylogenetically conserved family of genes that share a common DNA-binding domain, the T-box. T-box genes encode transcription factors involved in the regulation of developmental processes. Mutations in this gene have been associated with the inherited X-linked disorder, Cleft palate with ankyloglossia, and it is believed to play a major role in human palatogenesis. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BP7: Synonymous conserved (PhyloP=1.11 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TBX22	NM_001109878.2	c.106C>A	p.Arg36Arg	synonymous_variant	Exon 2 of 9	ENST00000373296.8	NP_001103348.1
TBX22	NM_016954.2	c.106C>A	p.Arg36Arg	synonymous_variant	Exon 1 of 8		NP_058650.1
TBX22	NM_001109879.2	c.-251C>A		5_prime_UTR_variant	Exon 2 of 9		NP_001103349.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TBX22	ENST00000373296.8	c.106C>A	p.Arg36Arg	synonymous_variant	Exon 2 of 9	5	NM_001109878.2	ENSP00000362393.3
TBX22	ENST00000373294.8	c.106C>A	p.Arg36Arg	synonymous_variant	Exon 1 of 8	1		ENSP00000362390.5
TBX22	ENST00000476373.1	n.227C>A		non_coding_transcript_exon_variant	Exon 2 of 2	3
TBX22	ENST00000626498.2	n.106C>A		non_coding_transcript_exon_variant	Exon 2 of 9	2		ENSP00000487527.1

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD3 exomes AF: 0.00000562 AC: 1 AN: 177999 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 63115

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000127

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000365 AC: 4 AN: 1096427 Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 1 AN XY: 361897

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000476

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	6.6
DANN	Benign	0.76

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: rs917472096; hg19: chrX-79277874;