NM_031923.4:c.409+69238T>C

Variant names:

• chr10-7893798-T-C
• rs10508338
• NM_031923.4:c.409+69238T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031923.4(TAF3):​c.409+69238T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 151,954 control chromosomes in the GnomAD database, including 27,517 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 0.59 (27517 hom., cov: 31)
• Consequence: TAF3 NM_031923.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132
• Publications: 4 publications found

Genes affected

TAF3 (HGNC:17303): (TATA-box binding protein associated factor 3) The highly conserved RNA polymerase II transcription factor TFIID (see TAF1; MIM 313650) comprises the TATA box-binding protein (TBP; MIM 600075) and a set of TBP-associated factors (TAFs), including TAF3. TAFs contribute to promoter recognition and selectivity and act as antiapoptotic factors (Gangloff et al., 2001 [PubMed 11438666]).[supplied by OMIM, May 2009]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031923.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAF3	NM_031923.4	MANE Select	c.409+69238T>C		intron	N/A	NP_114129.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAF3	ENST00000344293.6	TSL:1 MANE Select	c.409+69238T>C		intron	N/A	ENSP00000340271.5
	TAF3	ENST00000687522.1		c.409+69238T>C		intron	N/A	ENSP00000508875.1
	TAF3	ENST00000686593.1		n.413+69234T>C		intron	N/A	ENSP00000509355.1

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89608 AN: 151836 Hom.: 27507 Cov.: 31

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.590 AC: 89649 AN: 151954 Hom.: 27517 Cov.: 31 AF XY: 0.596 AC XY: 44282 AN XY: 74258

African (AFR) AF: 0.408 AC: 16879 AN: 41404

American (AMR) AF: 0.722 AC: 11023 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2419 AN: 3470

East Asian (EAS) AF: 0.711 AC: 3669 AN: 5160

South Asian (SAS) AF: 0.608 AC: 2930 AN: 4816

European-Finnish (FIN) AF: 0.672 AC: 7092 AN: 10552

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43485 AN: 67960

Other (OTH) AF: 0.623 AC: 1316 AN: 2114

Alfa AF: 0.619 Hom.: 56644

Bravo AF: 0.587

Asia WGS AF: 0.599 AC: 2084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.72
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10508338; hg19: chr10-7935761;