rs2585281

Positions:

• chr17-5229021-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SCIMP	NM_207103.3	c.22-5565A>G		intron_variant		ENST00000574081.6	NP_996986.1
ZNF594-DT	NR_034082.2	n.779-4803T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCIMP	ENST00000574081.6	c.22-5565A>G		intron_variant		1	NM_207103.3	ENSP00000461269	P1
ZNF594-DT	ENST00000573772.3	n.632+5537T>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.532

Alfa AF: 0.496 Hom.: 3112

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

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

Other links and lift over

dbSNP: rs2585281; hg19: chr17-5132316;