17-35822344-C-CA

Variant names:

• chr17-35822344-C-CA
• rs909362495
• NM_139215.3:c.291-278dupA

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_139215.3(TAF15):​c.291-278dupA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 67,276 control chromosomes in the GnomAD database, including 527 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.11 (527 hom., cov: 30)
• Consequence: TAF15 NM_139215.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.131
• Publications: 0 publications found

Genes affected

TAF15 (HGNC:11547): (TATA-box binding protein associated factor 15) This gene encodes a member of the TET family of RNA-binding proteins. The encoded protein plays a role in RNA polymerase II gene transcription as a component of a distinct subset of multi-subunit transcription initiation factor TFIID complexes. Translocations involving this gene play a role in acute leukemia and extraskeletal myxoid chondrosarcoma, and mutations in this gene may play a role in amyotrophic lateral sclerosis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, May 2012]

TAF15 Gene-Disease associations (from GenCC):

• amyotrophic lateral sclerosis

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ENSG00000270894 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 17-35822344-C-CA is Benign according to our data. Variant chr17-35822344-C-CA is described in ClinVar as Benign. ClinVar VariationId is 1183315.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_139215.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAF15	NM_139215.3	MANE Select	c.291-278dupA		intron	N/A	NP_631961.1	Q92804-1
	TAF15	NM_003487.4		c.282-278dupA		intron	N/A	NP_003478.1	Q92804-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAF15	ENST00000605844.6	TSL:1 MANE Select	c.291-296_291-295insA		intron	N/A	ENSP00000474096.1	Q92804-1
	TAF15	ENST00000604841.5	TSL:1	c.282-296_282-295insA		intron	N/A	ENSP00000474609.1	Q92804-2
	TAF15	ENST00000603393.6	TSL:1	n.291-296_291-295insA		intron	N/A	ENSP00000474653.2	A0A075B7E4

Frequencies

GnomAD3 genomes AF: 0.108 AC: 7244 AN: 67244 Hom.: 523 Cov.: 30

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0120

Gnomad EAS AF: 0.0640

Gnomad SAS AF: 0.00916

Gnomad FIN AF: 0.0249

Gnomad MID AF: 0.0851

Gnomad NFE AF: 0.0155

Gnomad OTH AF: 0.0972

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

GnomAD4 genome AF: 0.108 AC: 7266 AN: 67276 Hom.: 527 Cov.: 30 AF XY: 0.108 AC XY: 3439 AN XY: 31876

African (AFR) AF: 0.275 AC: 5754 AN: 20954

American (AMR) AF: 0.103 AC: 638 AN: 6192

Ashkenazi Jewish (ASJ) AF: 0.0120 AC: 18 AN: 1500

East Asian (EAS) AF: 0.0634 AC: 145 AN: 2286

South Asian (SAS) AF: 0.00915 AC: 20 AN: 2186

European-Finnish (FIN) AF: 0.0249 AC: 90 AN: 3616

Middle Eastern (MID) AF: 0.0870 AC: 8 AN: 92

European-Non Finnish (NFE) AF: 0.0155 AC: 451 AN: 29142

Other (OTH) AF: 0.0979 AC: 84 AN: 858

Alfa AF: 0.00287 Hom.: 2

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.13

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: rs909362495; hg19: chr17-34149348;