chr7-48052807-C-T

Variant names:

• chr7-48052807-C-T
• rs776631751
• NM_001100159.3:c.713C>T

Variant summary

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

The NM_001100159.3(C7orf57):​c.713C>T​(p.Thr238Ile) 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. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: C7orf57 NM_001100159.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.188
• Publications: 0 publications found

Genes affected

C7orf57 (HGNC:22247): (chromosome 7 open reading frame 57)

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=0.08702791).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001100159.3. 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
	C7orf57	NM_001100159.3	MANE Select	c.713C>T	p.Thr238Ile	missense	Exon 7 of 9	NP_001093629.1	Q8NEG2-1
	C7orf57	NM_001267865.2		c.299C>T	p.Thr100Ile	missense	Exon 6 of 8	NP_001254794.1	F5H7J8
	C7orf57	NM_001267866.2		c.299C>T	p.Thr100Ile	missense	Exon 6 of 7	NP_001254795.1	Q8NEG2-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C7orf57	ENST00000348904.4	TSL:1 MANE Select	c.713C>T	p.Thr238Ile	missense	Exon 7 of 9	ENSP00000335500.3	Q8NEG2-1
	C7orf57	ENST00000435376.5	TSL:1	c.299C>T	p.Thr100Ile	missense	Exon 6 of 7	ENSP00000391652.1	Q8NEG2-2
	C7orf57	ENST00000430738.5	TSL:5	c.848C>T	p.Thr283Ile	missense	Exon 7 of 9	ENSP00000410944.1	J3KQX6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

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	0.099
BayesDel_addAF	Benign	-0.19	T
BayesDel_noAF	Benign	-0.52
CADD	Benign	7.0
DANN	Uncertain	1.0
DEOGEN2	Benign	0.022	T
Eigen	Benign	-0.40
Eigen_PC	Benign	-0.48
FATHMM_MKL	Benign	0.086	N
LIST_S2	Benign	0.70	T
M_CAP	Benign	0.0070	T
MetaRNN	Benign	0.087	T
MetaSVM	Benign	-0.93	T
MutationAssessor	Uncertain	2.3	M
PhyloP100		0.19
PROVEAN	Benign	-1.9	N
REVEL	Benign	0.073
Sift	Benign	0.067	T
Sift4G	Benign	0.22	T
Polyphen		0.053	B
Vest4		0.15
MutPred		0.17		Loss of phosphorylation at T238 (P = 0.0093)
MVP		0.12
MPC		0.17
ClinPred		0.51	D
GERP RS		4.6
Varity_R		0.088
gMVP		0.18
Mutation Taster		=95/5	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: rs776631751; hg19: chr7-48092404;