Genetic Variant SCIMP:c.21+983C>T (chr17-5233752-G-A) – 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.21+983C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,232 control chromosomes in the GnomAD database, including 1,944 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 0.15 ( 1944 hom., cov: 32)

Exomes 𝑓: 0.077 ( 0 hom. )

Consequence

SCIMP
NM_207103.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0260

Publications

35 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:

Genome browser will be placed here

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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_207103.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SCIMP	NM_207103.3	MANE Select	c.21+983C>T	intron	N/A	NP_996986.1
SCIMP	NM_001271842.1		c.21+983C>T	intron	N/A	NP_001258771.1
SCIMP	NM_001319190.2		c.21+983C>T	intron	N/A	NP_001306119.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SCIMP	ENST00000574081.6	TSL:1 MANE Select	c.21+983C>T	intron	N/A	ENSP00000461269.1
SCIMP	ENST00000399600.8	TSL:1	c.21+983C>T	intron	N/A	ENSP00000382509.4
ZNF594-DT	ENST00000571689.1	TSL:1	n.682-72G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.148

AC:

22540

AN:

152036

Hom.:

1941

Cov.:

show subpopulations

Gnomad AFR

AF:

0.231

Gnomad AMI

AF:

0.0658

Gnomad AMR

AF:

0.0945

Gnomad ASJ

AF:

0.145

Gnomad EAS

AF:

0.0482

Gnomad SAS

AF:

0.0400

Gnomad FIN

AF:

0.192

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.130

GnomAD4 exome

AF:

0.0769

AC:

AN:

Hom.:

AF XY:

0.107

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.167

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0806

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.148

AC:

22560

AN:

152154

Hom.:

1944

Cov.:

AF XY:

0.150

AC XY:

11132

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.230

AC:

9569

AN:

41516

American (AMR)

AF:

0.0943

AC:

1441

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.145

AC:

503

AN:

3470

East Asian (EAS)

AF:

0.0479

AC:

248

AN:

5180

South Asian (SAS)

AF:

0.0402

AC:

194

AN:

4822

European-Finnish (FIN)

AF:

0.192

AC:

2034

AN:

10572

Middle Eastern (MID)

AF:

0.143

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.121

AC:

8196

AN:

67990

Other (OTH)

AF:

0.129

AC:

273

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

969

1937

2906

3874

4843

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

236

472

708

944

1180

<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:

0.126

Hom.:

2364

Bravo

AF:

0.145

Asia WGS

AF:

0.0490

AC:

171

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.3

(source)

DANN

Benign

0.60

PhyloP100

0.026

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over