chr17-5210283-C-T

Position:

• chr17-5210283-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25

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:):

ACMG classification

Verdict is Benign. Variant got -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	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCIMP	NM_207103.3	c.*518G>A		3_prime_UTR_variant	5/5	ENST00000574081.6	NP_996986.1
SCIMP	NM_001271842.1	c.*518G>A		3_prime_UTR_variant	5/5		NP_001258771.1
ZNF594-DT	NR_034082.2	n.303+388C>T		intron_variant
ZNF594-DT	NR_152840.1	n.303+388C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCIMP	ENST00000574081	c.*518G>A		3_prime_UTR_variant	5/5	1	NM_207103.3	ENSP00000461269.1

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72497 AN: 151630 Hom.: 20162 Cov.: 30

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.: 55 Cov.: 0 AF XY: 0.500 AC XY: 88 AN XY: 176

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.579

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0500

Gnomad4 FIN exome AF: 0.375

Gnomad4 NFE exome AF: 0.587

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.478 AC: 72503 AN: 151748 Hom.: 20159 Cov.: 30 AF XY: 0.466 AC XY: 34535 AN XY: 74140

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.580

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.644

Gnomad4 OTH AF: 0.546

Alfa AF: 0.615 Hom.: 29226

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
DANN	Benign	0.47

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: rs2641263; hg19: chr17-5113578;