11-93733700-G-C

Variant names:

• chr11-93733700-G-C
• rs2155248
• ENST00000526015.5:n.*57-195C>G

Variant summary

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

The ENST00000525928.5(TAF1D):​n.962C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000271 in 147,678 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000027 (0 hom., cov: 21)
  • Exomes 𝑓: 0.000024 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TAF1D ENST00000525928.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165
• Publications: 29 publications found

Genes affected

TAF1D (HGNC:28759): (TATA-box binding protein associated factor, RNA polymerase I subunit D) TAF1D is a member of the SL1 complex, which includes TBP (MIM 600075) and TAF1A (MIM 604903), TAF1B (MIM 604904), and TAF1C (MIM 604905), and plays a role in RNA polymerase I transcription (Wang et al., 2004 [PubMed 15520167]; Gorski et al., 2007 [PubMed 17318177]).[supplied by OMIM, Jun 2009]

MIR1304 (HGNC:35302): (microRNA 1304) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

SNORA18 (HGNC:32608): (small nucleolar RNA, H/ACA box 18)

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=-0.81).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000525928.5. 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
	MIR1304	NR_031639.1		n.65C>G		non_coding_transcript_exon	Exon 1 of 1
	TAF1D	NR_146090.2		n.1095-195C>G		intron	N/A
	TAF1D	NR_146091.2		n.1095-303C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAF1D	ENST00000526015.5	TSL:1	n.*57-195C>G		intron	N/A	ENSP00000435087.1	Q9H5J8
	MIR1304	ENST00000408243.1	TSL:6	n.65C>G		non_coding_transcript_exon	Exon 1 of 1
	TAF1D	ENST00000525928.5	TSL:2	n.962C>G		non_coding_transcript_exon	Exon 1 of 7

Frequencies

GnomAD3 genomes AF: 0.0000271 AC: 4 AN: 147678 Hom.: 0 Cov.: 21

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000601

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000296 AC: 5 AN: 168728 AF XY: 0.0000217

Gnomad AFR exome AF: 0.0000774

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000472

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000241 AC: 7 AN: 290778 Hom.: 0 Cov.: 0 AF XY: 0.0000181 AC XY: 3 AN XY: 165584

African (AFR) AF: 0.000130 AC: 1 AN: 7664

American (AMR) AF: 0.00 AC: 0 AN: 23064

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6696

East Asian (EAS) AF: 0.00 AC: 0 AN: 12568

South Asian (SAS) AF: 0.00 AC: 0 AN: 52446

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 13832

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2240

European-Non Finnish (NFE) AF: 0.0000315 AC: 5 AN: 158968

Other (OTH) AF: 0.0000752 AC: 1 AN: 13300

GnomAD4 genome AF: 0.0000271 AC: 4 AN: 147678 Hom.: 0 Cov.: 21 AF XY: 0.0000416 AC XY: 3 AN XY: 72142

African (AFR) AF: 0.00 AC: 0 AN: 39894

American (AMR) AF: 0.00 AC: 0 AN: 15072

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3428

East Asian (EAS) AF: 0.00 AC: 0 AN: 4714

South Asian (SAS) AF: 0.00 AC: 0 AN: 4510

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10282

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 304

European-Non Finnish (NFE) AF: 0.0000601 AC: 4 AN: 66540

Other (OTH) AF: 0.00 AC: 0 AN: 2030

Alfa AF: 0.000126 Hom.: 7517

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.0
DANN	Benign	0.82
PhyloP100		-0.17

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2155248; hg19: chr11-93466866;