chr6-50821738-T-C

Position:

• chr6-50821738-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_003221.4(TFAP2B):​c.82-1669T>C variant causes a intron change. The variant allele was found at a frequency of 0.607 in 171,014 control chromosomes in the GnomAD database, including 32,179 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 0.61 (28983 hom., cov: 31)
  • Exomes 𝑓: 0.56 (3196 hom.)
• Consequence: TFAP2B NM_003221.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.78

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]

TFAP2B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TFAP2B	NM_003221.4	c.82-1669T>C		intron_variant		ENST00000393655.4	NP_003212.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TFAP2B	ENST00000393655.4	c.82-1669T>C		intron_variant		1	NM_003221.4	ENSP00000377265.2
TFAP2B	ENST00000344788.7	c.49-396T>C		intron_variant		3		ENSP00000342252.3
TFAP2B	ENST00000489228.1	n.-47T>C		upstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93005 AN: 151774 Hom.: 28956 Cov.: 31

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.634

GnomAD4 exome AF: 0.560 AC: 10708 AN: 19122 Hom.: 3196 Cov.: 0 AF XY: 0.564 AC XY: 5736 AN XY: 10162

Gnomad4 AFR exome AF: 0.717

Gnomad4 AMR exome AF: 0.655

Gnomad4 ASJ exome AF: 0.602

Gnomad4 EAS exome AF: 0.579

Gnomad4 SAS exome AF: 0.606

Gnomad4 FIN exome AF: 0.557

Gnomad4 NFE exome AF: 0.523

Gnomad4 OTH exome AF: 0.533

GnomAD4 genome AF: 0.613 AC: 93088 AN: 151892 Hom.: 28983 Cov.: 31 AF XY: 0.615 AC XY: 45644 AN XY: 74250

Gnomad4 AFR AF: 0.718

Gnomad4 AMR AF: 0.637

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.635

Alfa AF: 0.540 Hom.: 5391

Bravo AF: 0.621

Asia WGS AF: 0.655 AC: 2277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	20
DANN	Benign	0.81

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: rs2076309; hg19: chr6-50789451;