rs3048712

Variant names:

• chrX-80022128-GGTTTTGTTTT-G
• rs3048712
• NM_001109878.2:c.-2-124_-2-115delGTTTTGTTTT

Your query was ambiguous. Multiple possible variants found:

• chrX-80022128-GGTTTTGTTTT-G
• chrX-80022128-GGTTTTGTTTT-GGTTTT
• chrX-80022128-GGTTTTGTTTT-GGTTTTGTTTTGTTTT
• chrX-80022128-GGTTTTGTTTT-GGTTTTGTTTTGTTTTGTTTT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001109878.2(TBX22):​c.-2-124_-2-115delGTTTTGTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000163 in 552,496 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0000094 (0 hom., 0 hem., cov: 6)
  • Exomes 𝑓: 0.000018 (0 hom. 5 hem.)
• Consequence: TBX22 NM_001109878.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.726

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 -4 ACMG points.

• BS2: High Hemizygotes in GnomAdExome4 at 5 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TBX22	NM_001109878.2	c.-2-124_-2-115delGTTTTGTTTT		intron_variant	Intron 1 of 8	ENST00000373296.8	NP_001103348.1
TBX22	NM_001109879.2	c.-358-124_-358-115delGTTTTGTTTT		intron_variant	Intron 1 of 8		NP_001103349.1
TBX22	NM_016954.2	c.-141_-132delGTTTTGTTTT		upstream_gene_variant			NP_058650.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TBX22	ENST00000373296.8	c.-2-139_-2-130delGTTTTGTTTT		intron_variant	Intron 1 of 8	5	NM_001109878.2	ENSP00000362393.3
TBX22	ENST00000476373.1	n.120-139_120-130delGTTTTGTTTT		intron_variant	Intron 1 of 1	3
TBX22	ENST00000626498.2	n.-2-139_-2-130delGTTTTGTTTT		intron_variant	Intron 1 of 8	2		ENSP00000487527.1
TBX22	ENST00000373294.8	c.-141_-132delGTTTTGTTTT		upstream_gene_variant		1		ENSP00000362390.5

Frequencies

GnomAD3 genomes AF: 0.00000937 AC: 1 AN: 106765 Hom.: 0 Cov.: 6 AF XY: 0.00 AC XY: 0 AN XY: 29543

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000101

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: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000179 AC: 8 AN: 445687 Hom.: 0 AF XY: 0.0000359 AC XY: 5 AN XY: 139163

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000118

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000946

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000103

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000936 AC: 1 AN: 106809 Hom.: 0 Cov.: 6 AF XY: 0.00 AC XY: 0 AN XY: 29599

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.000101

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3048712; hg19: chrX-79277627;