Variant chr6-70836999-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001044305.3(SMAP1):c.635C>T(p.Ala212Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 1,598,686 control chromosomes in the GnomAD database, including 16,583 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.17 ( 3326 hom., cov: 32)

Exomes 𝑓: 0.10 ( 13257 hom. )

Consequence

SMAP1
NM_001044305.3 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.446

Variant links:

Genes affected

SMAP1 (HGNC:19651): (small ArfGAP 1) The protein encoded by this gene is similar to the mouse stromal membrane-associated protein-1. This similarity suggests that this human gene product is also a type II membrane glycoprotein involved in the erythropoietic stimulatory activity of stromal cells. Alternate splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

SMAP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=9.086791E-5).

BP6

Variant 6-70836999-C-T is Benign according to our data. Variant chr6-70836999-C-T is described in ClinVar as [Benign]. Clinvar id is 1297961.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMAP1	NM_001044305.3 linkuse as main transcript	c.635C>T	p.Ala212Val	missense_variant	7/11	ENST00000370455.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMAP1	ENST00000370455.8 linkuse as main transcript	c.635C>T	p.Ala212Val	missense_variant	7/11	1	NM_001044305.3	P3	Q8IYB5-1

Frequencies

GnomAD3 genomes

AF:

0.167

AC:

25344

AN:

151948

Hom.:

3324

Cov.:

show subpopulations

Gnomad AFR

AF:

0.300

Gnomad AMI

AF:

0.0844

Gnomad AMR

AF:

0.162

Gnomad ASJ

AF:

0.0652

Gnomad EAS

AF:

0.566

Gnomad SAS

AF:

0.177

Gnomad FIN

AF:

0.0904

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.0748

Gnomad OTH

AF:

0.146

GnomAD3 exomes

AF:

0.154

AC:

36914

AN:

239392

Hom.:

5090

AF XY:

0.146

AC XY:

18868

AN XY:

129486

show subpopulations

Gnomad AFR exome

AF:

0.292

Gnomad AMR exome

AF:

0.207

Gnomad ASJ exome

AF:

0.0679

Gnomad EAS exome

AF:

0.577

Gnomad SAS exome

AF:

0.152

Gnomad FIN exome

AF:

0.0859

Gnomad NFE exome

AF:

0.0767

Gnomad OTH exome

AF:

0.122

GnomAD4 exome

AF:

0.103

AC:

148522

AN:

1446620

Hom.:

13257

Cov.:

AF XY:

0.103

AC XY:

74032

AN XY:

718850

show subpopulations

Gnomad4 AFR exome

AF:

0.299

Gnomad4 AMR exome

AF:

0.204

Gnomad4 ASJ exome

AF:

0.0683

Gnomad4 EAS exome

AF:

0.533

Gnomad4 SAS exome

AF:

0.153

Gnomad4 FIN exome

AF:

0.0861

Gnomad4 NFE exome

AF:

0.0745

Gnomad4 OTH exome

AF:

0.124

GnomAD4 genome

AF:

0.167

AC:

25380

AN:

152066

Hom.:

3326

Cov.:

AF XY:

0.169

AC XY:

12589

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.300

Gnomad4 AMR

AF:

0.162

Gnomad4 ASJ

AF:

0.0652

Gnomad4 EAS

AF:

0.566

Gnomad4 SAS

AF:

0.176

Gnomad4 FIN

AF:

0.0904

Gnomad4 NFE

AF:

0.0748

Gnomad4 OTH

AF:

0.152

Alfa

AF:

0.0958

Hom.:

2512

Bravo

AF:

0.182

TwinsUK

AF:

0.0693

AC:

257

ALSPAC

AF:

0.0786

AC:

303

ESP6500AA

AF:

0.291

AC:

1280

ESP6500EA

AF:

0.0751

AC:

646

ExAC

AF:

0.155

AC:

18829

Asia WGS

AF:

0.344

AC:

1193

AN:

3476

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

GeneDx

Jun 24, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.075

BayesDel_addAF

Benign

-0.68

BayesDel_noAF

Benign

-0.61

CADD

Benign

DANN

Benign

0.85

DEOGEN2

Benign

0.022

.;.;T;.

Eigen

Benign

-0.79

Eigen_PC

Benign

-0.65

FATHMM_MKL

Benign

0.64

LIST_S2

Benign

0.77

T;T;T;T

MetaRNN

Benign

0.000091

T;T;T;T

MetaSVM

Benign

-0.96

MutationAssessor

Benign

0.81

.;.;L;.

MutationTaster

Benign

0.76

P;P;P

PrimateAI

Benign

0.33

PROVEAN

Benign

-1.7

N;N;N;.

REVEL

Benign

0.038

Sift

Benign

0.20

T;T;T;.

Sift4G

Benign

0.34

T;T;T;T

Polyphen

0.66

P;B;B;.

Vest4

0.049

MPC

0.12

ClinPred

0.0091

GERP RS

3.4

Varity_R

0.038

gMVP

0.19

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over