rs2585281

Variant names:

• chr17-5229021-T-C
• rs2585281
• NM_207103.3:c.22-5565A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_207103.3(SCIMP):​c.22-5565A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 152,040 control chromosomes in the GnomAD database, including 19,600 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 0.46 (19600 hom., cov: 31)
• Consequence: SCIMP NM_207103.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.873
• Publications: 7 publications found

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]

ZNF594-DT (HGNC:55347): (ZNF594 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCIMP	NM_207103.3	c.22-5565A>G		intron_variant	Intron 1 of 4	ENST00000574081.6	NP_996986.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCIMP	ENST00000574081.6	c.22-5565A>G		intron_variant	Intron 1 of 4	1	NM_207103.3	ENSP00000461269.1

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70572 AN: 151922 Hom.: 19604 Cov.: 31

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.537

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.464 AC: 70577 AN: 152040 Hom.: 19600 Cov.: 31 AF XY: 0.452 AC XY: 33580 AN XY: 74318

African (AFR) AF: 0.182 AC: 7538 AN: 41474

American (AMR) AF: 0.575 AC: 8762 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2103 AN: 3468

East Asian (EAS) AF: 0.178 AC: 918 AN: 5168

South Asian (SAS) AF: 0.262 AC: 1263 AN: 4828

European-Finnish (FIN) AF: 0.448 AC: 4744 AN: 10580

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43488 AN: 67956

Other (OTH) AF: 0.532 AC: 1125 AN: 2116

Alfa AF: 0.485 Hom.: 3129

Bravo AF: 0.466

Asia WGS AF: 0.211 AC: 736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.9
DANN	Benign	0.75
PhyloP100		-0.87
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2585281; hg19: chr17-5132316;