rs606462

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr11-93754252-C-A
• chr11-93754252-C-G
• chr11-93754252-C-T

Variant summary

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

The NM_001286069.2(C11orf54):​c.330+215C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: 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=-0.88).

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>A		intron	N/A	NP_001272998.1	Q9H0W9-1
	C11orf54	NM_001286067.2		c.330+215C>A		intron	N/A	NP_001272996.1	Q9H0W9-1
	C11orf54	NM_001286068.2		c.330+215C>A		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>A		intron	N/A	ENSP00000346403.3	Q9H0W9-1
	ENSG00000284057	ENST00000638767.1	TSL:5	c.231+215C>A		intron	N/A	ENSP00000492220.1	A0A1W2PRB8
	C11orf54	ENST00000331239.8	TSL:1	c.330+215C>A		intron	N/A	ENSP00000331209.4	Q9H0W9-1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.73
DANN	Benign	0.15
PhyloP100		-0.45

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;