rs16867195

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr2-9849313-A-G
• chr2-9849313-A-T

Variant summary

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

The ENST00000263663.10(TAF1B):​c.118-60A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 1,297,138 control chromosomes in the GnomAD database, including 56,937 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 0.24 (5002 hom., cov: 32)
  • Exomes 𝑓: 0.30 (51935 hom.)
• Consequence: TAF1B ENST00000263663.10 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000263663.10. 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>G		intron	N/A	NP_005671.3
	TAF1B	NM_001318976.1		c.-494-60A>G		intron	N/A	NP_001305905.1
	TAF1B	NM_001318977.1		c.-494-60A>G		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>G		intron	N/A	ENSP00000263663.4
	TAF1B	ENST00000402170.5	TSL:5	n.178-60A>G		intron	N/A
	TAF1B	ENST00000404869.7	TSL:5	n.163-60A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36759 AN: 151940 Hom.: 5005 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.250

GnomAD4 exome AF: 0.297 AC: 339767 AN: 1145080 Hom.: 51935 AF XY: 0.295 AC XY: 169226 AN XY: 573798

African (AFR) AF: 0.112 AC: 2654 AN: 23766

American (AMR) AF: 0.224 AC: 4187 AN: 18662

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 5579 AN: 22092

East Asian (EAS) AF: 0.334 AC: 11109 AN: 33304

South Asian (SAS) AF: 0.251 AC: 15758 AN: 62854

European-Finnish (FIN) AF: 0.331 AC: 15617 AN: 47228

Middle Eastern (MID) AF: 0.203 AC: 1039 AN: 5124

European-Non Finnish (NFE) AF: 0.306 AC: 270392 AN: 883116

Other (OTH) AF: 0.274 AC: 13432 AN: 48934

GnomAD4 genome AF: 0.242 AC: 36748 AN: 152058 Hom.: 5002 Cov.: 32 AF XY: 0.244 AC XY: 18097 AN XY: 74302

African (AFR) AF: 0.118 AC: 4893 AN: 41510

American (AMR) AF: 0.221 AC: 3379 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3470

East Asian (EAS) AF: 0.305 AC: 1576 AN: 5170

South Asian (SAS) AF: 0.257 AC: 1240 AN: 4818

European-Finnish (FIN) AF: 0.334 AC: 3517 AN: 10534

Middle Eastern (MID) AF: 0.195 AC: 57 AN: 292

European-Non Finnish (NFE) AF: 0.301 AC: 20458 AN: 67962

Other (OTH) AF: 0.246 AC: 519 AN: 2110

Alfa AF: 0.280 Hom.: 19977

Bravo AF: 0.229

Asia WGS AF: 0.254 AC: 886 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.5
DANN	Benign	0.49
PhyloP100		0.19
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: rs16867195; hg19: chr2-9989442; COSMIC: COSV55153897; COSMIC: COSV55153897;