Variant 1-244378525-G-C 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_001012970.3(C1orf100):c.211G>C(p.Asp71His) variant causes a missense change. The variant allele was found at a frequency of 0.00468 in 1,613,838 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0031 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0048 ( 22 hom. )

Consequence

C1orf100
NM_001012970.3 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.29

Variant links:

Genes affected

C1orf100 (HGNC:):

C1orf100 links:

SPMIP3 (HGNC:30435): (sperm microtubule inner protein 3)

SPMIP3 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=0.028751194).

BP6

Variant 1-244378525-G-C is Benign according to our data. Variant chr1-244378525-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 2640222.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 22 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C1orf100	NM_001012970.3 linkuse as main transcript	c.211G>C	p.Asp71His	missense_variant	4/5	ENST00000308105.5	NP_001012988.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPMIP3	ENST00000308105.5 linkuse as main transcript	c.211G>C	p.Asp71His	missense_variant	4/5	2	NM_001012970.3	ENSP00000311218	P1	Q5SVJ3-1
	ENST00000417765.1 linkuse as main transcript	n.158-2062C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.00313

AC:

476

AN:

152098

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000942

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00164

Gnomad ASJ

AF:

0.00288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000830

Gnomad FIN

AF:

0.00180

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00540

Gnomad OTH

AF:

0.00527

GnomAD3 exomes

AF:

0.00335

AC:

841

AN:

251398

Hom.:

AF XY:

0.00352

AC XY:

478

AN XY:

135858

show subpopulations

Gnomad AFR exome

AF:

0.00129

Gnomad AMR exome

AF:

0.00197

Gnomad ASJ exome

AF:

0.00635

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000817

Gnomad FIN exome

AF:

0.00194

Gnomad NFE exome

AF:

0.00518

Gnomad OTH exome

AF:

0.00522

GnomAD4 exome

AF:

0.00484

AC:

7075

AN:

1461622

Hom.:

Cov.:

AF XY:

0.00483

AC XY:

3515

AN XY:

727136

show subpopulations

Gnomad4 AFR exome

AF:

0.000986

Gnomad4 AMR exome

AF:

0.00233

Gnomad4 ASJ exome

AF:

0.00551

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000777

Gnomad4 FIN exome

AF:

0.00213

Gnomad4 NFE exome

AF:

0.00570

Gnomad4 OTH exome

AF:

0.00404

GnomAD4 genome

AF:

0.00313

AC:

476

AN:

152216

Hom.:

Cov.:

AF XY:

0.00266

AC XY:

198

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.000939

Gnomad4 AMR

AF:

0.00164

Gnomad4 ASJ

AF:

0.00288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000831

Gnomad4 FIN

AF:

0.00180

Gnomad4 NFE

AF:

0.00540

Gnomad4 OTH

AF:

0.00521

Alfa

AF:

0.00493

Hom.:

Bravo

AF:

0.00315

TwinsUK

AF:

0.00836

AC:

ALSPAC

AF:

0.00389

AC:

ESP6500AA

AF:

0.00113

AC:

ESP6500EA

AF:

0.00651

AC:

ExAC

AF:

0.00338

AC:

411

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00551

EpiControl

AF:

0.00652

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Dec 01, 2022

SPMIP3: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.81

BayesDel_addAF

Uncertain

0.068

BayesDel_noAF

Pathogenic

0.33

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.31

Eigen

Uncertain

0.57

Eigen_PC

Uncertain

0.49

FATHMM_MKL

Uncertain

0.92

LIST_S2

Benign

0.63

MetaRNN

Benign

0.029

MetaSVM

Benign

-0.36

MutationAssessor

Uncertain

2.6

MutationTaster

Benign

0.99

D;D

PROVEAN

Pathogenic

-6.0

REVEL

Uncertain

0.42

Sift

Pathogenic

0.0

Sift4G

Pathogenic

0.0

Polyphen

1.0

Vest4

0.89

MVP

0.076

MPC

0.33

ClinPred

0.023

GERP RS

4.9

Varity_R

0.82

gMVP

0.61

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over