rs1284108

Variant names:

• chr11-93765667-G-T
• rs1284108
• ENST00000638767.1:c.675+5809G>T

Variant summary

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

The ENST00000638767.1(ENSG00000284057):​c.675+5809G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 152,144 control chromosomes in the GnomAD database, including 24,806 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 0.55 (24806 hom., cov: 34)
• Consequence: ENSG00000284057 ENST00000638767.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629
• Publications: 32 publications found

Genes affected

ENSG00000284057 (HGNC:):

C11orf54 (HGNC:30204): (chromosome 11 open reading frame 54) Enables hydrolase activity, acting on ester bonds and zinc ion binding activity. Located in nuclear body. [provided by Alliance of Genome Resources, Apr 2022]

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000638767.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000284057	ENST00000638767.1	TSL:5	c.675+5809G>T		intron	N/A	ENSP00000492220.1	A0A1W2PRB8
	C11orf54	ENST00000951671.1		c.*38-1219G>T		intron	N/A	ENSP00000621730.1
	TAF1D	ENST00000527690.1	TSL:3	c.-224+18637C>A		intron	N/A	ENSP00000432852.1	A0A1D5RMT6

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84311 AN: 152028 Hom.: 24791 Cov.: 34

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.575

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.554 AC: 84348 AN: 152144 Hom.: 24806 Cov.: 34 AF XY: 0.561 AC XY: 41708 AN XY: 74386

African (AFR) AF: 0.340 AC: 14091 AN: 41500

American (AMR) AF: 0.691 AC: 10567 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2103 AN: 3464

East Asian (EAS) AF: 0.642 AC: 3322 AN: 5176

South Asian (SAS) AF: 0.587 AC: 2832 AN: 4822

European-Finnish (FIN) AF: 0.673 AC: 7128 AN: 10596

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42407 AN: 67976

Other (OTH) AF: 0.572 AC: 1209 AN: 2114

Alfa AF: 0.603 Hom.: 118931

Bravo AF: 0.547

Asia WGS AF: 0.552 AC: 1919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.22
PhyloP100		-0.63

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1284108;

hg19: chr11-93498833;