rs3833842

Positions:

• chr16-30086868-GTGATGA-G
• chr16-30086868-GTGATGA-GTGA
• chr16-30086868-GTGATGA-GTGATGATGA
• chr16-30086868-GTGATGA-GTGATGATGATGA

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP6_Moderate

The NM_004608.4(TBX6):​c.840-23_840-18del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000988 in 1,599,794 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.000046 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00010 (0 hom.)
• Consequence: TBX6 NM_004608.4 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.06

Genes affected

TBX6 (HGNC:11605): (T-box transcription factor 6) 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. Knockout studies in mice indicate that this gene is important for specification of paraxial mesoderm structures. [provided by RefSeq, Aug 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant 16-30086868-GTGATGA-G is Benign according to our data. Variant chr16-30086868-GTGATGA-G is described in ClinVar as [Likely_benign]. Clinvar id is 1615180.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TBX6	NM_004608.4	c.840-23_840-18del		intron_variant		ENST00000395224.7
TBX6	XM_011545926.4	c.840-23_840-18del		intron_variant
TBX6	XM_047434551.1	c.840-23_840-18del		intron_variant
TBX6	XR_007064904.1	n.1038_1043del		non_coding_transcript_exon_variant	7/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TBX6	ENST00000395224.7	c.840-23_840-18del		intron_variant		1	NM_004608.4	P1
TBX6	ENST00000279386.6	c.840-23_840-18del		intron_variant		1		P1
TBX6	ENST00000567664.5	c.*48-179_*48-174del		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0000461 AC: 7 AN: 151724 Hom.: 0 Cov.: 0

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: 0.000103

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000104 AC: 151 AN: 1447952 Hom.: 0 AF XY: 0.000110 AC XY: 79 AN XY: 719516

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000689

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000118

Gnomad4 FIN exome AF: 0.0000200

Gnomad4 NFE exome AF: 0.000118

Gnomad4 OTH exome AF: 0.0000668

GnomAD4 genome AF: 0.0000461 AC: 7 AN: 151842 Hom.: 0 Cov.: 0 AF XY: 0.0000674 AC XY: 5 AN XY: 74196

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: 0.000103

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000141 Hom.: 1171

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Oct 13, 2023

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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: rs3833842; hg19: chr16-30098189;