19-55489062-G-GCC

Position:

• chr19-55489062-G-GCC

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP6

The NM_001144950.2(SSC5D):​c.52+40_52+41dupCC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.00030 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00014 (0 hom.)
• Consequence: SSC5D NM_001144950.2 intron
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: -1.08

Genes affected

SSC5D (HGNC:26641): (scavenger receptor cysteine rich family member with 5 domains) Predicted to enable fibronectin binding activity; laminin binding activity; and scavenger receptor activity. Predicted to be involved in defense response; detection of bacterial lipoprotein; and negative regulation of interleukin-8 production. Predicted to act upstream of or within regulation of interleukin-8 production. Predicted to be located in collagen-containing extracellular matrix. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

SSC5D (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -1 ACMG points.

• BP6: Variant 19-55489062-G-GCC is Benign according to our data. Variant chr19-55489062-G-GCC is described in ClinVar as [Likely_benign]. Clinvar id is 3050761.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SSC5D	NM_001144950.2	c.52+40_52+41dupCC		intron_variant		ENST00000389623.11	NP_001138422.1
SSC5D	NM_001195267.2	c.52+40_52+41dupCC		intron_variant			NP_001182196.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SSC5D	ENST00000389623.11	c.52+40_52+41dupCC		intron_variant		1	NM_001144950.2	ENSP00000374274.4
SSC5D	ENST00000587166.5	c.52+40_52+41dupCC		intron_variant		1		ENSP00000467252.1
SSC5D	ENST00000594321.5	c.52+40_52+41dupCC		intron_variant		4		ENSP00000470226.1
SSC5D	ENST00000588254.1	n.185_186dupCC		non_coding_transcript_exon_variant	2/5	2

Frequencies

GnomAD3 genomes AF: 0.000287 AC: 30 AN: 104476 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000933

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000185

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00109

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000195

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000101 AC: 2 AN: 19718 Hom.: 0 AF XY: 0.0000992 AC XY: 1 AN XY: 10082

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000732

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000137 AC: 111 AN: 807466 Hom.: 0 Cov.: 0 AF XY: 0.000135 AC XY: 54 AN XY: 398694

Gnomad4 AFR exome AF: 0.000966

Gnomad4 AMR exome AF: 0.000183

Gnomad4 ASJ exome AF: 0.0000734

Gnomad4 EAS exome AF: 0.00242

Gnomad4 SAS exome AF: 0.000204

Gnomad4 FIN exome AF: 0.0000264

Gnomad4 NFE exome AF: 0.0000446

Gnomad4 OTH exome AF: 0.000201

GnomAD4 genome AF: 0.000297 AC: 31 AN: 104528 Hom.: 0 Cov.: 0 AF XY: 0.000303 AC XY: 15 AN XY: 49520

Gnomad4 AFR AF: 0.000969

Gnomad4 AMR AF: 0.000185

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00110

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000195

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

SSC5D-related disorder Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 20, 2020

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs57080356; hg19: chr19-56000429;