rs7225151

chr17-5233752-G-A

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCIMP	NM_207103.3	c.21+983C>T		intron_variant		ENST00000574081.6
ZNF594-DT	NR_034082.2	n.779-72G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCIMP	ENST00000574081.6	c.21+983C>T		intron_variant		1	NM_207103.3	P1
ZNF594-DT	ENST00000573772.3	n.632+10268G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22540 AN: 152036 Hom.: 1941 Cov.: 32

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: 6 AN: 78 Hom.: 0 AF XY: 0.107 AC XY: 6 AN XY: 56

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.167

Gnomad4 NFE exome AF: 0.0806

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.148 AC: 22560 AN: 152154 Hom.: 1944 Cov.: 32 AF XY: 0.150 AC XY: 11132 AN XY: 74382

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.0943

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.0479

Gnomad4 SAS AF: 0.0402

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.129

Alfa AF: 0.123 Hom.: 1607

Bravo AF: 0.145

Asia WGS AF: 0.0490 AC: 171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.3
Dann	Benign	0.60

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: rs7225151; hg19: chr17-5137047;