chr17-35822344-CA-C

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_139215.3(TAF15):​c.291-278delA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.014 (11 hom., cov: 30)
  • Failed GnomAD Quality Control
• Consequence: TAF15 NM_139215.3 intron
• Clinical Significance: Likely 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: Likely_benign. The variant received -2 ACMG points.

• BP6: Variant 17-35822344-CA-C is Benign according to our data. Variant chr17-35822344-CA-C is described in ClinVar as Likely_benign. ClinVar VariationId is 1216247.Status of the report is criteria_provided_single_submitter, 1 stars.

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.291-278delA		intron	N/A	NP_631961.1	Q92804-1
	TAF15	NM_003487.4		c.282-278delA		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.291-295delA		intron	N/A	ENSP00000474096.1	Q92804-1
	TAF15	ENST00000604841.5	TSL:1	c.282-295delA		intron	N/A	ENSP00000474609.1	Q92804-2
	TAF15	ENST00000603393.6	TSL:1	n.291-295delA		intron	N/A	ENSP00000474653.2	A0A075B7E4

Frequencies

GnomAD3 genomes AF: 0.0140 AC: 941 AN: 67426 Hom.: 11 Cov.: 30

Gnomad AFR AF: 0.00510

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00841

Gnomad ASJ AF: 0.00332

Gnomad EAS AF: 0.0157

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.0925

Gnomad MID AF: 0.0319

Gnomad NFE AF: 0.00619

Gnomad OTH AF: 0.00468

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0139 AC: 940 AN: 67458 Hom.: 11 Cov.: 30 AF XY: 0.0184 AC XY: 587 AN XY: 31942

African (AFR) AF: 0.00509 AC: 107 AN: 21008

American (AMR) AF: 0.00840 AC: 52 AN: 6190

Ashkenazi Jewish (ASJ) AF: 0.00332 AC: 5 AN: 1506

East Asian (EAS) AF: 0.0157 AC: 36 AN: 2288

South Asian (SAS) AF: 0.0996 AC: 218 AN: 2188

European-Finnish (FIN) AF: 0.0925 AC: 334 AN: 3612

Middle Eastern (MID) AF: 0.0326 AC: 3 AN: 92

European-Non Finnish (NFE) AF: 0.00619 AC: 181 AN: 29264

Other (OTH) AF: 0.00466 AC: 4 AN: 858

Alfa AF: 0.000936 Hom.: 2

ClinVar

ClinVar submissions

Significance: Likely 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
Mutation Taster		=100/0	polymorphism

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs909362495;

hg19: chr17-34149348;