Variant chr6-50818858-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The XR_007059923.1(LOC124901490):n.125+44C>T variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.126 in 1,600,400 control chromosomes in the GnomAD database, including 15,106 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.17 ( 2795 hom., cov: 32)

Exomes 𝑓: 0.12 ( 12311 hom. )

Consequence

LOC124901490
XR_007059923.1 intron, non_coding_transcript

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 6.23

Variant links:

Genes affected

LOC124901490 (HGNC:):

LOC124901490 links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.39).

BP6

Variant 6-50818858-G-A is Benign according to our data. Variant chr6-50818858-G-A is described in ClinVar as [Benign]. Clinvar id is 1273651.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901490	XR_007059923.1 linkuse as main transcript	n.125+44C>T		intron_variant, non_coding_transcript_variant
TFAP2B	NM_003221.4 linkuse as main transcript			upstream_gene_variant		ENST00000393655.4	NP_003212.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TFAP2B	ENST00000344788.7 linkuse as main transcript	c.-67G>A		5_prime_UTR_variant	1/4	3		ENSP00000342252
TFAP2B	ENST00000393655.4 linkuse as main transcript			upstream_gene_variant		1	NM_003221.4	ENSP00000377265	P1	Q92481-1

Frequencies

GnomAD3 genomes

AF:

0.173

AC:

26273

AN:

151822

Hom.:

2792

Cov.:

show subpopulations

Gnomad AFR

AF:

0.291

Gnomad AMI

AF:

0.0681

Gnomad AMR

AF:

0.145

Gnomad ASJ

AF:

0.176

Gnomad EAS

AF:

0.208

Gnomad SAS

AF:

0.192

Gnomad FIN

AF:

0.192

Gnomad MID

AF:

0.158

Gnomad NFE

AF:

0.102

Gnomad OTH

AF:

0.169

GnomAD3 exomes

AF:

0.149

AC:

37476

AN:

250704

Hom.:

3292

AF XY:

0.149

AC XY:

20223

AN XY:

135502

show subpopulations

Gnomad AFR exome

AF:

0.295

Gnomad AMR exome

AF:

0.118

Gnomad ASJ exome

AF:

0.171

Gnomad EAS exome

AF:

0.228

Gnomad SAS exome

AF:

0.192

Gnomad FIN exome

AF:

0.187

Gnomad NFE exome

AF:

0.105

Gnomad OTH exome

AF:

0.154

GnomAD4 exome

AF:

0.122

AC:

176025

AN:

1448460

Hom.:

12311

Cov.:

AF XY:

0.123

AC XY:

88848

AN XY:

721588

show subpopulations

Gnomad4 AFR exome

AF:

0.299

Gnomad4 AMR exome

AF:

0.121

Gnomad4 ASJ exome

AF:

0.167

Gnomad4 EAS exome

AF:

0.226

Gnomad4 SAS exome

AF:

0.189

Gnomad4 FIN exome

AF:

0.175

Gnomad4 NFE exome

AF:

0.102

Gnomad4 OTH exome

AF:

0.136

GnomAD4 genome

AF:

0.173

AC:

26288

AN:

151940

Hom.:

2795

Cov.:

AF XY:

0.179

AC XY:

13294

AN XY:

74268

show subpopulations

Gnomad4 AFR

AF:

0.290

Gnomad4 AMR

AF:

0.146

Gnomad4 ASJ

AF:

0.176

Gnomad4 EAS

AF:

0.207

Gnomad4 SAS

AF:

0.192

Gnomad4 FIN

AF:

0.192

Gnomad4 NFE

AF:

0.102

Gnomad4 OTH

AF:

0.168

Alfa

AF:

0.128

Hom.:

1017

Bravo

AF:

0.175

Asia WGS

AF:

0.182

AC:

632

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Char syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 10, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

DANN

Benign

0.93

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over