chr11-6210514-C-T

Variant names:

• chr11-6210514-C-T
• rs1037161461
• NM_173525.3:c.737C>T

Variant summary

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

The NM_173525.3(C11orf42):​c.737C>T​(p.Thr246Ile) 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. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: C11orf42 NM_173525.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.0750
• Publications: 1 publications found

Genes affected

C11orf42 (HGNC:28541): (chromosome 11 open reading frame 42)

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 (MetaRNN=0.041276902).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173525.3. 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
	C11orf42	NM_173525.3	MANE Select	c.737C>T	p.Thr246Ile	missense	Exon 2 of 3	NP_775796.2	Q8N5U0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C11orf42	ENST00000316375.3	TSL:1 MANE Select	c.737C>T	p.Thr246Ile	missense	Exon 2 of 3	ENSP00000321021.2	Q8N5U0

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

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	Benign	0.091
BayesDel_addAF	Benign	-0.35	T
BayesDel_noAF	Benign	-0.74
CADD	Benign	7.7
DANN	Benign	0.71
DEOGEN2	Benign	0.017	T
Eigen	Benign	-1.0
Eigen_PC	Benign	-0.97
FATHMM_MKL	Benign	0.015	N
LIST_S2	Benign	0.39	T
M_CAP	Benign	0.0034	T
MetaRNN	Benign	0.041	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.34	N
PhyloP100		0.075
PROVEAN	Benign	-0.87	N
REVEL	Benign	0.018
Sift	Benign	0.48	T
Sift4G	Benign	0.48	T
Polyphen		0.0080	B
Vest4		0.088
MutPred		0.21		Loss of glycosylation at T246 (P = 0.0025)
MVP		0.28
MPC		0.11
ClinPred		0.023	T
GERP RS		0.89
Varity_R		0.034
gMVP		0.13
Mutation Taster		=99/1	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

dbSNP: rs1037161461; hg19: chr11-6231744; COSMIC: COSV56409886; COSMIC: COSV56409886;