chr2-9849313-A-T

Variant names:

• chr2-9849313-A-T
• rs16867195
• NM_005680.3:c.118-60A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_005680.3(TAF1B):​c.118-60A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TAF1B NM_005680.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188
• Publications: 6 publications found

Genes affected

TAF1B (HGNC:11533): (TATA-box binding protein associated factor, RNA polymerase I subunit B) Initiation of transcription by RNA polymerase I requires the formation of a complex composed of the TATA-binding protein (TBP) and three TBP-associated factors (TAFs) specific for RNA polymerase I. This complex, known as SL1, binds to the core promoter of ribosomal RNA genes to position the polymerase properly and acts as a channel for regulatory signals. This gene encodes one of the SL1-specific TAFs. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2016]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005680.3. 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
	TAF1B	NM_005680.3	MANE Select	c.118-60A>T		intron	N/A	NP_005671.3
	TAF1B	NM_001318976.1		c.-494-60A>T		intron	N/A	NP_001305905.1
	TAF1B	NM_001318977.1		c.-494-60A>T		intron	N/A	NP_001305906.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAF1B	ENST00000263663.10	TSL:1 MANE Select	c.118-60A>T		intron	N/A	ENSP00000263663.4
	TAF1B	ENST00000944452.1		c.118-60A>T		intron	N/A	ENSP00000614511.1
	TAF1B	ENST00000402170.5	TSL:5	n.178-60A>T		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1147790 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 575084

African (AFR) AF: 0.00 AC: 0 AN: 23804

American (AMR) AF: 0.00 AC: 0 AN: 18712

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22118

East Asian (EAS) AF: 0.00 AC: 0 AN: 33360

South Asian (SAS) AF: 0.00 AC: 0 AN: 62980

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 47316

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5130

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 885338

Other (OTH) AF: 0.00 AC: 0 AN: 49032

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.8
DANN	Benign	0.54
PhyloP100		0.19

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: rs16867195; hg19: chr2-9989442;