chr16-84178112-C-T

Variant names:

• chr16-84178112-C-T
• rs1056616
• NM_001243156.2:c.*829G>A

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001243156.2(TAF1C):​c.*829G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 435,124 control chromosomes in the GnomAD database, including 4,512 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.15 (1982 hom., cov: 32)
  • Exomes 𝑓: 0.12 (2530 hom.)
• Consequence: TAF1C NM_001243156.2 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.03

Genes affected

TAF1C (HGNC:11534): (TATA-box binding protein associated factor, RNA polymerase I subunit C) 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 the largest SL1-specific TAF. Multiple alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2011]

DNAAF1 (HGNC:30539): (dynein axonemal assembly factor 1) The protein encoded by this gene is cilium-specific and is required for the stability of the ciliary architecture. It is involved in the regulation of microtubule-based cilia and actin-based brush border microvilli. Mutations in this gene are associated with primary ciliary dyskinesia-13. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 16-84178112-C-T is Benign according to our data. Variant chr16-84178112-C-T is described in ClinVar as [Benign]. Clinvar id is 1237217.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAF1C	NM_001243156.2	c.*829G>A		3_prime_UTR_variant	Exon 15 of 15	ENST00000566732.6	NP_001230085.2
DNAAF1	NM_178452.6	c.*271C>T		downstream_gene_variant		ENST00000378553.10	NP_848547.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAF1C	ENST00000566732.6	c.*829G>A		3_prime_UTR_variant	Exon 15 of 15	2	NM_001243156.2	ENSP00000455933.1
DNAAF1	ENST00000378553.10	c.*271C>T		downstream_gene_variant		1	NM_178452.6	ENSP00000367815.5

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22101 AN: 151808 Hom.: 1976 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.0813

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0924

Gnomad OTH AF: 0.151

GnomAD4 exome AF: 0.121 AC: 34395 AN: 283198 Hom.: 2530 Cov.: 0 AF XY: 0.129 AC XY: 19867 AN XY: 153904

African (AFR) AF: 0.234 AC: 1866 AN: 7970

American (AMR) AF: 0.0773 AC: 1153 AN: 14922

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 1133 AN: 7960

East Asian (EAS) AF: 0.204 AC: 2965 AN: 14516

South Asian (SAS) AF: 0.202 AC: 8900 AN: 43996

European-Finnish (FIN) AF: 0.0916 AC: 1256 AN: 13718

Middle Eastern (MID) AF: 0.131 AC: 171 AN: 1304

European-Non Finnish (NFE) AF: 0.0926 AC: 15171 AN: 163792

Other (OTH) AF: 0.119 AC: 1780 AN: 15020

GnomAD4 genome AF: 0.146 AC: 22134 AN: 151926 Hom.: 1982 Cov.: 32 AF XY: 0.145 AC XY: 10751 AN XY: 74248

African (AFR) AF: 0.249 AC: 10289 AN: 41342

American (AMR) AF: 0.108 AC: 1648 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 502 AN: 3468

East Asian (EAS) AF: 0.213 AC: 1102 AN: 5164

South Asian (SAS) AF: 0.204 AC: 981 AN: 4798

European-Finnish (FIN) AF: 0.0813 AC: 858 AN: 10556

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0924 AC: 6284 AN: 68002

Other (OTH) AF: 0.156 AC: 329 AN: 2114

Alfa AF: 0.112 Hom.: 1995

Bravo AF: 0.149

Asia WGS AF: 0.223 AC: 775 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.26
DANN	Benign	0.51
PhyloP100		-2.0
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

Publications

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Other links and lift over

dbSNP: rs1056616; hg19: chr16-84211718;