Variant 17-5223379-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_207103.3(SCIMP):c.99T>C(p.Gly33Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 1,611,498 control chromosomes in the GnomAD database, including 347,473 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).

Frequency

Genomes: 𝑓 0.56 ( 25854 hom., cov: 30)

Exomes 𝑓: 0.65 ( 321619 hom. )

Consequence

SCIMP
NM_207103.3 synonymous

Scores

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: 0.436

Variant links:

Genes affected

SCIMP (HGNC:33504): (SLP adaptor and CSK interacting membrane protein) This gene encodes a transmembrane adaptor protein that is expressed in antigen-presenting cells and is localized in the immunologic synapse. The encoded protein is involved in major histocompatibility complex class II signal transduction and immune synapse formation. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2012]

SCIMP links:

ZNF594-DT (HGNC:):

ZNF594-DT links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BP7

Synonymous conserved (PhyloP=0.436 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCIMP	NM_207103.3 linkuse as main transcript	c.99T>C	p.Gly33Gly	synonymous_variant	2/5	ENST00000574081.6	NP_996986.1	Q6UWF3-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCIMP	ENST00000574081.6 linkuse as main transcript	c.99T>C	p.Gly33Gly	synonymous_variant	2/5	1	NM_207103.3	ENSP00000461269.1		Q6UWF3-1

Frequencies

GnomAD3 genomes

AF:

0.563

AC:

85303

AN:

151430

Hom.:

25853

Cov.:

show subpopulations

Gnomad AFR

AF:

0.362

Gnomad AMI

AF:

0.532

Gnomad AMR

AF:

0.636

Gnomad ASJ

AF:

0.646

Gnomad EAS

AF:

0.338

Gnomad SAS

AF:

0.347

Gnomad FIN

AF:

0.544

Gnomad MID

AF:

0.618

Gnomad NFE

AF:

0.699

Gnomad OTH

AF:

0.613

GnomAD3 exomes

AF:

0.582

AC:

144730

AN:

248566

Hom.:

45023

AF XY:

0.580

AC XY:

78270

AN XY:

134912

show subpopulations

Gnomad AFR exome

AF:

0.349

Gnomad AMR exome

AF:

0.612

Gnomad ASJ exome

AF:

0.642

Gnomad EAS exome

AF:

0.345

Gnomad SAS exome

AF:

0.357

Gnomad FIN exome

AF:

0.555

Gnomad NFE exome

AF:

0.701

Gnomad OTH exome

AF:

0.626

GnomAD4 exome

AF:

0.653

AC:

953208

AN:

1459950

Hom.:

321619

Cov.:

AF XY:

0.645

AC XY:

468716

AN XY:

726286

show subpopulations

Gnomad4 AFR exome

AF:

0.337

Gnomad4 AMR exome

AF:

0.615

Gnomad4 ASJ exome

AF:

0.651

Gnomad4 EAS exome

AF:

0.314

Gnomad4 SAS exome

AF:

0.369

Gnomad4 FIN exome

AF:

0.569

Gnomad4 NFE exome

AF:

0.704

Gnomad4 OTH exome

AF:

0.624

GnomAD4 genome

AF:

0.563

AC:

85327

AN:

151548

Hom.:

25854

Cov.:

AF XY:

0.552

AC XY:

40860

AN XY:

74044

show subpopulations

Gnomad4 AFR

AF:

0.362

Gnomad4 AMR

AF:

0.635

Gnomad4 ASJ

AF:

0.646

Gnomad4 EAS

AF:

0.338

Gnomad4 SAS

AF:

0.349

Gnomad4 FIN

AF:

0.544

Gnomad4 NFE

AF:

0.699

Gnomad4 OTH

AF:

0.606

Alfa

AF:

0.668

Hom.:

60880

Bravo

AF:

0.566

Asia WGS

AF:

0.328

AC:

1145

AN:

3478

EpiCase

AF:

0.703

EpiControl

AF:

0.704

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Head and neck cancer

Uncertain:1

Uncertain significance, no assertion criteria provided

research

Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University

Jun 10, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

DANN

Benign

0.83

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

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