chr11-8925587-C-T

Variant names:

• chr11-8925587-C-T
• NM_020643.3:c.1080G>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_020643.3(C11orf16):​c.1080G>A​(p.Met360Ile) variant causes a missense 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. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 34)
• Consequence: C11orf16 NM_020643.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.236
• Publications: 0 publications found

Genes affected

C11orf16 (HGNC:1169): (chromosome 11 open reading frame 16)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.093940884).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020643.3. 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
	C11orf16	NM_020643.3	MANE Select	c.1080G>A	p.Met360Ile	missense	Exon 5 of 7	NP_065694.2	Q9NQ32-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C11orf16	ENST00000326053.10	TSL:1 MANE Select	c.1080G>A	p.Met360Ile	missense	Exon 5 of 7	ENSP00000318999.5	Q9NQ32-1
	C11orf16	ENST00000525780.5	TSL:1	c.1080G>A	p.Met360Ile	missense	Exon 5 of 6	ENSP00000436818.1	Q9NQ32-2

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 69

GnomAD4 genome Cov.: 34

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.39
BayesDel_addAF	Benign	-0.19	T
BayesDel_noAF	Benign	-0.51
CADD	Benign	19
DANN	Uncertain	0.98
DEOGEN2	Benign	0.021	T
Eigen	Benign	-0.070
Eigen_PC	Benign	0.010
FATHMM_MKL	Benign	0.25	N
LIST_S2	Benign	0.73	T
M_CAP	Benign	0.0058	T
MetaRNN	Benign	0.094	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.4	L
PhyloP100		0.24
PROVEAN	Benign	-1.9	N
REVEL	Benign	0.048
Sift	Benign	0.15	T
Sift4G	Benign	0.13	T
Polyphen		0.40	B
Vest4		0.099
MutPred		0.27		Loss of disorder (P = 0.0389)
MVP		0.26
MPC		0.038
ClinPred		0.70	D
GERP RS		4.7
Varity_R		0.56
gMVP		0.082
Mutation Taster		=93/7	polymorphism

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

hg19: chr11-8947134;