Genetic Variant SSC5D:p.Thr1310Thr (chr19-55518206-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7

The NM_001144950.2(SSC5D):c.3930C>T(p.Thr1310Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0021 ( 0 hom., cov: 21)

Exomes 𝑓: 0.00078 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

SSC5D
NM_001144950.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0140

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 19-55518206-C-T is Benign according to our data. Variant chr19-55518206-C-T is described in ClinVar as [Benign]. Clinvar id is 403488.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.014 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSC5D	NM_001144950.2 link	c.3930C>T	p.Thr1310Thr	synonymous_variant	Exon 14 of 14	ENST00000389623.11	NP_001138422.1	A1L4H1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SSC5D	ENST00000389623.11 link	c.3930C>T	p.Thr1310Thr	synonymous_variant	Exon 14 of 14	1	NM_001144950.2	ENSP00000374274.4		A1L4H1-1

Frequencies

GnomAD3 genomes

AF:

0.00207

AC:

228

AN:

110394

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00764

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00198

Gnomad ASJ

AF:

0.00104

Gnomad EAS

AF:

0.000993

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000637

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000433

Gnomad OTH

AF:

0.00330

GnomAD3 exomes

AF:

0.00155

AC:

196

AN:

126818

Hom.:

AF XY:

0.00123

AC XY:

AN XY:

68434

show subpopulations

Gnomad AFR exome

AF:

0.0107

Gnomad AMR exome

AF:

0.00423

Gnomad ASJ exome

AF:

0.00128

Gnomad EAS exome

AF:

0.00157

Gnomad SAS exome

AF:

0.000140

Gnomad FIN exome

AF:

0.00123

Gnomad NFE exome

AF:

0.000619

Gnomad OTH exome

AF:

0.00109

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000780

AC:

1025

AN:

1314156

Hom.:

Cov.:

AF XY:

0.000709

AC XY:

459

AN XY:

647764

show subpopulations

Gnomad4 AFR exome

AF:

0.0154

Gnomad4 AMR exome

AF:

0.00228

Gnomad4 ASJ exome

AF:

0.000842

Gnomad4 EAS exome

AF:

0.000500

Gnomad4 SAS exome

AF:

0.0000921

Gnomad4 FIN exome

AF:

0.000202

Gnomad4 NFE exome

AF:

0.000392

Gnomad4 OTH exome

AF:

0.00150

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00208

AC:

230

AN:

110452

Hom.:

Cov.:

AF XY:

0.00222

AC XY:

119

AN XY:

53676

show subpopulations

Gnomad4 AFR

AF:

0.00771

Gnomad4 AMR

AF:

0.00197

Gnomad4 ASJ

AF:

0.00104

Gnomad4 EAS

AF:

0.000993

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000637

Gnomad4 NFE

AF:

0.000433

Gnomad4 OTH

AF:

0.00325

Alfa

AF:

0.0373

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.99

DANN

Benign

0.41

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over