Variant 1-151142531-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_030913.6(SEMA6C):c.91C>T(p.Leu31Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00825 in 1,613,176 control chromosomes in the GnomAD database, including 64 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0055 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0085 ( 61 hom. )

Consequence

SEMA6C
NM_030913.6 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.468

Variant links:

Genes affected

SEMA6C (HGNC:10740): (semaphorin 6C) This gene encodes a member of the semaphorin family. Semaphorins represent important molecular signals controlling multiple aspects of the cellular response that follows CNS injury, and thus may play an important role in neural regeneration. [provided by RefSeq, May 2010]

SEMA6C links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.00812459).

BP6

Variant 1-151142531-G-A is Benign according to our data. Variant chr1-151142531-G-A is described in ClinVar as [Benign]. Clinvar id is 770327.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SEMA6C	NM_030913.6 link	c.91C>T	p.Leu31Phe	missense_variant	3/19	ENST00000368914.8	NP_112175.2	Q9H3T2-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SEMA6C	ENST00000368914.8 link	c.91C>T	p.Leu31Phe	missense_variant	3/19	1	NM_030913.6	ENSP00000357910.3	Q9H3T2-1
SEMA6C	ENST00000368913.7 link	c.91C>T	p.Leu31Phe	missense_variant	3/20	1		ENSP00000357909.3	Q9H3T2-3
SEMA6C	ENST00000341697.7 link	c.91C>T	p.Leu31Phe	missense_variant	3/19	1		ENSP00000344148.3	Q9H3T2-1
SEMA6C	ENST00000368912.7 link	c.91C>T	p.Leu31Phe	missense_variant	3/19	1		ENSP00000357908.3	Q9H3T2-2

Frequencies

GnomAD3 genomes

AF:

0.00551

AC:

838

AN:

152174

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00140

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.00419

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.00292

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00967

Gnomad OTH

AF:

0.00431

GnomAD3 exomes

AF:

0.00613

AC:

1520

AN:

247824

Hom.:

AF XY:

0.00614

AC XY:

821

AN XY:

133680

show subpopulations

Gnomad AFR exome

AF:

0.00144

Gnomad AMR exome

AF:

0.00218

Gnomad ASJ exome

AF:

0.000614

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00271

Gnomad FIN exome

AF:

0.00380

Gnomad NFE exome

AF:

0.0109

Gnomad OTH exome

AF:

0.00555

GnomAD4 exome

AF:

0.00853

AC:

12468

AN:

1460884

Hom.:

Cov.:

AF XY:

0.00838

AC XY:

6092

AN XY:

726680

show subpopulations

Gnomad4 AFR exome

AF:

0.00120

Gnomad4 AMR exome

AF:

0.00215

Gnomad4 ASJ exome

AF:

0.00112

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00273

Gnomad4 FIN exome

AF:

0.00457

Gnomad4 NFE exome

AF:

0.0103

Gnomad4 OTH exome

AF:

0.00641

GnomAD4 genome

AF:

0.00550

AC:

838

AN:

152292

Hom.:

Cov.:

AF XY:

0.00532

AC XY:

396

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.00140

Gnomad4 AMR

AF:

0.00418

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00207

Gnomad4 FIN

AF:

0.00292

Gnomad4 NFE

AF:

0.00967

Gnomad4 OTH

AF:

0.00426

Alfa

AF:

0.00907

Hom.:

Bravo

AF:

0.00530

TwinsUK

AF:

0.0102

AC:

ALSPAC

AF:

0.00882

AC:

ESP6500AA

AF:

0.00182

AC:

ESP6500EA

AF:

0.00977

AC:

ExAC

AF:

0.00693

AC:

841

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00791

EpiControl

AF:

0.00896

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 05, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.080

BayesDel_addAF

Benign

-0.62

BayesDel_noAF

Benign

-0.66

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.062

.;.;T;T;T;T

Eigen

Benign

-0.45

Eigen_PC

Benign

-0.32

FATHMM_MKL

Benign

0.46

LIST_S2

Uncertain

0.86

D;D;.;D;T;T

MetaRNN

Benign

0.0081

T;T;T;T;T;T

MetaSVM

Benign

-0.96

MutationAssessor

Benign

0.69

N;N;N;N;.;.

PrimateAI

Benign

0.31

PROVEAN

Benign

-0.93

N;N;N;N;.;.

REVEL

Benign

0.0090

Sift

Benign

0.036

D;D;D;D;.;.

Sift4G

Benign

0.43

T;T;T;T;T;T

Polyphen

0.068

B;B;B;B;.;.

Vest4

0.34

MVP

0.26

MPC

0.49

ClinPred

0.0074

GERP RS

1.6

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Varity_R

0.041

gMVP

0.36

Splicing

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over