11-93754252-C-G

Variant names:

• chr11-93754252-C-G
• rs606462
• NM_001286069.2:c.330+215C>G

Variant summary

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

The NM_001286069.2(C11orf54):​c.330+215C>G 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 151,978 control chromosomes in the GnomAD database, including 24,761 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 (24761 hom., cov: 32)
• Consequence: C11orf54 NM_001286069.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453
• Publications: 7 publications found

Genes affected

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]

ENSG00000284057 (HGNC:):

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=-0.93).
• 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: NM_001286069.2. 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
	C11orf54	NM_001286069.2	MANE Select	c.330+215C>G		intron	N/A	NP_001272998.1	Q9H0W9-1
	C11orf54	NM_001286067.2		c.330+215C>G		intron	N/A	NP_001272996.1	Q9H0W9-1
	C11orf54	NM_001286068.2		c.330+215C>G		intron	N/A	NP_001272997.1	Q9H0W9-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C11orf54	ENST00000354421.8	TSL:1 MANE Select	c.330+215C>G		intron	N/A	ENSP00000346403.3	Q9H0W9-1
	ENSG00000284057	ENST00000638767.1	TSL:5	c.231+215C>G		intron	N/A	ENSP00000492220.1	A0A1W2PRB8
	C11orf54	ENST00000331239.8	TSL:1	c.330+215C>G		intron	N/A	ENSP00000331209.4	Q9H0W9-1

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84199 AN: 151860 Hom.: 24746 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.554 AC: 84237 AN: 151978 Hom.: 24761 Cov.: 32 AF XY: 0.561 AC XY: 41628 AN XY: 74264

African (AFR) AF: 0.339 AC: 14069 AN: 41460

American (AMR) AF: 0.691 AC: 10553 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2093 AN: 3470

East Asian (EAS) AF: 0.644 AC: 3321 AN: 5160

South Asian (SAS) AF: 0.587 AC: 2834 AN: 4824

European-Finnish (FIN) AF: 0.673 AC: 7091 AN: 10544

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

European-Non Finnish (NFE) AF: 0.624 AC: 42383 AN: 67944

Other (OTH) AF: 0.571 AC: 1206 AN: 2112

Alfa AF: 0.452 Hom.: 1349

Bravo AF: 0.547

Asia WGS AF: 0.551 AC: 1918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.77
DANN	Benign	0.52
PhyloP100		-0.45
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: rs606462; hg19: chr11-93487418;