Genetic Variant SCIMP:c.*518G>A (chr17-5210283-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_207103.3(SCIMP):c.*518G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 152,092 control chromosomes in the GnomAD database, including 20,214 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.

Frequency

Genomes: 𝑓 0.48 ( 20159 hom., cov: 30)

Exomes 𝑓: 0.53 ( 55 hom. )

Consequence

SCIMP
NM_207103.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.25

Publications

15 publications found

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:55347): (ZNF594 divergent transcript)

ZNF594-DT links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
SCIMP	NM_207103.3 link	c.*518G>A	3_prime_UTR_variant	Exon 5 of 5	ENST00000574081.6	NP_996986.1
SCIMP	NM_001271842.1 link	c.*518G>A	3_prime_UTR_variant	Exon 5 of 5		NP_001258771.1
ZNF594-DT	NR_034082.2 link	n.303+388C>T	intron_variant	Intron 2 of 7
ZNF594-DT	NR_152840.1 link	n.303+388C>T	intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCIMP	ENST00000574081.6 link	c.*518G>A		3_prime_UTR_variant	Exon 5 of 5	1	NM_207103.3	ENSP00000461269.1

Frequencies

GnomAD3 genomes

AF:

0.478

AC:

72497

AN:

151630

Hom.:

20162

Cov.:

show subpopulations

Gnomad AFR

AF:

0.218

Gnomad AMI

AF:

0.520

Gnomad AMR

AF:

0.580

Gnomad ASJ

AF:

0.611

Gnomad EAS

AF:

0.161

Gnomad SAS

AF:

0.278

Gnomad FIN

AF:

0.460

Gnomad MID

AF:

0.541

Gnomad NFE

AF:

0.644

Gnomad OTH

AF:

0.552

GnomAD4 exome

AF:

0.532

AC:

183

AN:

344

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

176

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.579

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.0500

AC:

AN:

European-Finnish (FIN)

AF:

0.375

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.587

AC:

149

AN:

254

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.543

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.478

AC:

72503

AN:

151748

Hom.:

20159

Cov.:

AF XY:

0.466

AC XY:

34535

AN XY:

74140

show subpopulations

African (AFR)

AF:

0.218

AC:

9007

AN:

41346

American (AMR)

AF:

0.580

AC:

8826

AN:

15214

Ashkenazi Jewish (ASJ)

AF:

0.611

AC:

2120

AN:

3470

East Asian (EAS)

AF:

0.161

AC:

829

AN:

5158

South Asian (SAS)

AF:

0.280

AC:

1349

AN:

4810

European-Finnish (FIN)

AF:

0.460

AC:

4848

AN:

10528

Middle Eastern (MID)

AF:

0.554

AC:

163

AN:

294

European-Non Finnish (NFE)

AF:

0.644

AC:

43734

AN:

67906

Other (OTH)

AF:

0.546

AC:

1154

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1650

3300

4949

6599

8249

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

614

1228

1842

2456

3070

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.600

Hom.:

36751

Bravo

AF:

0.480

Asia WGS

AF:

0.217

AC:

755

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

4.6

(source)

DANN

Benign

0.47

PhyloP100

1.3

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over