Variant rs2242655 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_021184.4(C6orf47):c.276G>C(p.Lys92Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 1,612,968 control chromosomes in the GnomAD database, including 17,000 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.14 ( 1740 hom., cov: 32)

Exomes 𝑓: 0.14 ( 15260 hom. )

Consequence

C6orf47
NM_021184.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.451

Variant links:

Genes affected

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

C6orf47 links:

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

C6orf47-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0035974681).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C6orf47	NM_021184.4 linkuse as main transcript	c.276G>C	p.Lys92Asn	missense_variant	1/1	ENST00000375911.2	NP_067007.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C6orf47	ENST00000375911.2 linkuse as main transcript	c.276G>C	p.Lys92Asn	missense_variant	1/1		NM_021184.4	ENSP00000365076	P1
C6orf47-AS1	ENST00000422049.1 linkuse as main transcript	n.352-728C>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.135

AC:

20589

AN:

152122

Hom.:

1736

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0807

Gnomad AMI

AF:

0.136

Gnomad AMR

AF:

0.188

Gnomad ASJ

AF:

0.0300

Gnomad EAS

AF:

0.147

Gnomad SAS

AF:

0.104

Gnomad FIN

AF:

0.329

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.135

Gnomad OTH

AF:

0.107

GnomAD3 exomes

AF:

0.152

AC:

37393

AN:

246464

Hom.:

3582

AF XY:

0.145

AC XY:

19441

AN XY:

134370

show subpopulations

Gnomad AFR exome

AF:

0.0811

Gnomad AMR exome

AF:

0.234

Gnomad ASJ exome

AF:

0.0290

Gnomad EAS exome

AF:

0.141

Gnomad SAS exome

AF:

0.101

Gnomad FIN exome

AF:

0.313

Gnomad NFE exome

AF:

0.132

Gnomad OTH exome

AF:

0.138

GnomAD4 exome

AF:

0.135

AC:

197583

AN:

1460728

Hom.:

15260

Cov.:

AF XY:

0.133

AC XY:

96501

AN XY:

726678

show subpopulations

Gnomad4 AFR exome

AF:

0.0693

Gnomad4 AMR exome

AF:

0.224

Gnomad4 ASJ exome

AF:

0.0308

Gnomad4 EAS exome

AF:

0.215

Gnomad4 SAS exome

AF:

0.101

Gnomad4 FIN exome

AF:

0.310

Gnomad4 NFE exome

AF:

0.129

Gnomad4 OTH exome

AF:

0.122

GnomAD4 genome

AF:

0.135

AC:

20612

AN:

152240

Hom.:

1740

Cov.:

AF XY:

0.144

AC XY:

10698

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.0806

Gnomad4 AMR

AF:

0.189

Gnomad4 ASJ

AF:

0.0300

Gnomad4 EAS

AF:

0.147

Gnomad4 SAS

AF:

0.104

Gnomad4 FIN

AF:

0.329

Gnomad4 NFE

AF:

0.135

Gnomad4 OTH

AF:

0.106

Alfa

AF:

0.121

Hom.:

950

Bravo

AF:

0.125

TwinsUK

AF:

0.129

AC:

479

ALSPAC

AF:

0.124

AC:

478

ESP6500AA

AF:

0.0851

AC:

257

ESP6500EA

AF:

0.134

AC:

724

ExAC

AF:

0.146

AC:

17102

Asia WGS

AF:

0.141

AC:

491

AN:

3478

EpiCase

AF:

0.113

EpiControl

AF:

0.115

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.37

BayesDel_addAF

Benign

-0.69

BayesDel_noAF

Benign

-0.62

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.020

Eigen

Uncertain

0.21

Eigen_PC

Benign

0.15

FATHMM_MKL

Benign

0.15

LIST_S2

Benign

0.37

MetaRNN

Benign

0.0036

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.97

MutationTaster

Benign

0.96

PROVEAN

Uncertain

-2.7

REVEL

Benign

0.060

Sift

Uncertain

0.0060

Sift4G

Uncertain

0.018

Polyphen

0.98

Vest4

0.030

MutPred

0.14

Loss of ubiquitination at K92 (P = 0.0047);

MPC

0.78

ClinPred

0.015

GERP RS

3.5

Varity_R

0.095

gMVP

0.035

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over