rs4800250

Positions:

• chr18-26230803-G-A

Variant summary

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

The NM_005640.3(TAF4B):​c.343+3527G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 151,980 control chromosomes in the GnomAD database, including 33,671 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 0.64 (33671 hom., cov: 30)
• Consequence: TAF4B NM_005640.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310

Genes affected

TAF4B (HGNC:11538): (TATA-box binding protein associated factor 4b) TATA binding protein (TBP) and TBP-associated factors (TAFs) participate in the formation of the TFIID protein complex, which is involved in initiation of transcription of genes by RNA polymerase II. This gene encodes a cell type-specific TAF that may be responsible for mediating transcription by a subset of activators in B cells. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jun 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAF4B	NM_005640.3	c.343+3527G>A		intron_variant		ENST00000269142.10	NP_005631.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAF4B	ENST00000269142.10	c.343+3527G>A		intron_variant		1	NM_005640.3	ENSP00000269142	P4
TAF4B	ENST00000578121.5	c.343+3527G>A		intron_variant		2		ENSP00000462980	A2
TAF4B	ENST00000418698.3	c.343+3527G>A		intron_variant, NMD_transcript_variant		5		ENSP00000389365

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97803 AN: 151862 Hom.: 33615 Cov.: 30

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.644 AC: 97902 AN: 151980 Hom.: 33671 Cov.: 30 AF XY: 0.634 AC XY: 47090 AN XY: 74266

Gnomad4 AFR AF: 0.874

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.609

Alfa AF: 0.589 Hom.: 13582

Bravo AF: 0.656

Asia WGS AF: 0.360 AC: 1254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.63

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: rs4800250; hg19: chr18-23810767;