C6orf47 p.Lys92Asn

Variant names:

• chr6-31659672-C-A
• NM_021184.4:c.276G>T
• C6orf47 p.Lys92Asn

Your query was ambiguous. Multiple possible variants found:

• chr6-31659672-C-A
• chr6-31659672-C-G

Variant summary

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

The NM_021184.4(C6orf47):​c.276G>T​(p.Lys92Asn) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: C6orf47 NM_021184.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.451
• Publications: 0 publications found

Genes affected

C6orf47 (HGNC:19076): (chromosome 6 open reading frame 47)

C6orf47-AS1 (HGNC:39767): (C6orf47 antisense RNA 1)

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=0.16255206).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021184.4. 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
	C6orf47	NM_021184.4	MANE Select	c.276G>T	p.Lys92Asn	missense	Exon 1 of 1	NP_067007.3	A0A1U9X7F2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C6orf47	ENST00000375911.2	TSL:6 MANE Select	c.276G>T	p.Lys92Asn	missense	Exon 1 of 1	ENSP00000365076.1	O95873
	C6orf47-AS1	ENST00000422049.1	TSL:2	n.352-728C>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.37
BayesDel_addAF	Benign	-0.27	T
BayesDel_noAF	Benign	-0.62
CADD	Benign	22
DANN	Uncertain	1.0
DEOGEN2	Benign	0.020	T
Eigen	Uncertain	0.21
Eigen_PC	Benign	0.15
FATHMM_MKL	Benign	0.16	N
LIST_S2	Benign	0.37	T
M_CAP	Benign	0.016	T
MetaRNN	Benign	0.16	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.97	L
PhyloP100		0.45
PROVEAN	Uncertain	-2.7	D
REVEL	Benign	0.063
Sift	Uncertain	0.0060	D
Sift4G	Uncertain	0.018	D
Varity_R		0.095
gMVP		0.035
Mutation Taster		=100/0	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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr6-31627449;