chr6-50824094-A-T

Position:

• chr6-50824094-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003221.4(TFAP2B):​c.540+229A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,276 control chromosomes in the GnomAD database, including 983 homozygotes. 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 0.10 (983 hom., cov: 33)
• Consequence: TFAP2B NM_003221.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.896

Genes affected

TFAP2B (HGNC:11743): (transcription factor AP-2 beta) This gene encodes a member of the AP-2 family of transcription factors. AP-2 proteins form homo- or hetero-dimers with other AP-2 family members and bind specific DNA sequences. They are thought to stimulate cell proliferation and suppress terminal differentiation of specific cell types during embryonic development. Specific AP-2 family members differ in their expression patterns and binding affinity for different promoters. This protein functions as both a transcriptional activator and repressor. Mutations in this gene result in autosomal dominant Char syndrome, suggesting that this gene functions in the differentiation of neural crest cell derivatives. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TFAP2B	NM_003221.4	c.540+229A>T		intron_variant		ENST00000393655.4	NP_003212.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TFAP2B	ENST00000393655.4	c.540+229A>T		intron_variant		1	NM_003221.4	ENSP00000377265	P1
TFAP2B	ENST00000344788.7	c.534+229A>T		intron_variant		3		ENSP00000342252

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15910 AN: 152158 Hom.: 981 Cov.: 33

Gnomad AFR AF: 0.0544

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0995

Gnomad FIN AF: 0.0774

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.129

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.105 AC: 15920 AN: 152276 Hom.: 983 Cov.: 33 AF XY: 0.100 AC XY: 7479 AN XY: 74456

Gnomad4 AFR AF: 0.0546

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0995

Gnomad4 FIN AF: 0.0774

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.127

Alfa AF: 0.118 Hom.: 136

Bravo AF: 0.103

Asia WGS AF: 0.0480 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	9.4
DANN	Benign	0.74

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: rs7771651; hg19: chr6-50791807;