ENST00000526015.5:n.*57-195C>A

Variant names:

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

Variant summary

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

The ENST00000526015.5(TAF1D):​n.*57-195C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.951 in 438,510 control chromosomes in the GnomAD database, including 200,248 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 0.90 (61277 hom., cov: 21)
  • Exomes 𝑓: 0.98 (138971 hom.)
• Consequence: TAF1D ENST00000526015.5 intron
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.984 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000526015.5. 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
	MIR1304	NR_031639.1		n.65C>A		non_coding_transcript_exon	Exon 1 of 1
	TAF1D	NR_146090.2		n.1095-195C>A		intron	N/A
	TAF1D	NR_146091.2		n.1095-303C>A		intron	N/A

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.902 AC: 133202 AN: 147622 Hom.: 61253 Cov.: 21

Gnomad AFR AF: 0.696

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.971

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.989

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.899

GnomAD2 exomes AF: 0.958 AC: 161647 AN: 168728 AF XY: 0.964

Gnomad AFR exome AF: 0.687

Gnomad AMR exome AF: 0.970

Gnomad ASJ exome AF: 0.971

Gnomad EAS exome AF: 0.939

Gnomad FIN exome AF: 1.00

Gnomad NFE exome AF: 0.990

Gnomad OTH exome AF: 0.961

GnomAD4 exome AF: 0.976 AC: 283887 AN: 290766 Hom.: 138971 Cov.: 0 AF XY: 0.979 AC XY: 162026 AN XY: 165576

African (AFR) AF: 0.692 AC: 5301 AN: 7660

American (AMR) AF: 0.970 AC: 22364 AN: 23062

Ashkenazi Jewish (ASJ) AF: 0.970 AC: 6494 AN: 6696

East Asian (EAS) AF: 0.938 AC: 11783 AN: 12568

South Asian (SAS) AF: 0.986 AC: 51704 AN: 52446

European-Finnish (FIN) AF: 0.999 AC: 13816 AN: 13832

Middle Eastern (MID) AF: 0.924 AC: 2069 AN: 2240

European-Non Finnish (NFE) AF: 0.991 AC: 157500 AN: 158966

Other (OTH) AF: 0.967 AC: 12856 AN: 13296

GnomAD4 genome AF: 0.902 AC: 133280 AN: 147744 Hom.: 61277 Cov.: 21 AF XY: 0.904 AC XY: 65317 AN XY: 72246

African (AFR) AF: 0.696 AC: 27813 AN: 39970

American (AMR) AF: 0.934 AC: 14091 AN: 15086

Ashkenazi Jewish (ASJ) AF: 0.971 AC: 3330 AN: 3428

East Asian (EAS) AF: 0.944 AC: 4442 AN: 4704

South Asian (SAS) AF: 0.990 AC: 4459 AN: 4506

European-Finnish (FIN) AF: 0.999 AC: 10274 AN: 10282

Middle Eastern (MID) AF: 0.904 AC: 255 AN: 282

European-Non Finnish (NFE) AF: 0.990 AC: 65863 AN: 66528

Other (OTH) AF: 0.900 AC: 1849 AN: 2054

Alfa AF: 0.960 Hom.: 7517

Bravo AF: 0.886

Asia WGS AF: 0.950 AC: 3305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.9
DANN	Benign	0.86
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;