7-76393715-A-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_080744.2(SSC4D):ā€‹c.1023T>Gā€‹(p.Ser341Arg) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000255 in 1,386,882 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: š‘“ 0.000040 ( 0 hom., cov: 34)
Exomes š‘“: 0.00028 ( 0 hom. )

Consequence

SSC4D
NM_080744.2 missense, splice_region

Scores

1
3
15
Splicing: ADA: 0.002869
2

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.0650
Variant links:
Genes affected
SSC4D (HGNC:14461): (scavenger receptor cysteine rich family member with 4 domains) The scavenger receptor cysteine-rich (SRCR) superfamily is an ancient and highly conserved group of cell surface and/or secreted proteins, some of which are involved in the development of the immune system and the regulation of both innate and adaptive immune responses. Group B SRCR domains usually contain 8 regularly spaced cysteines that give rise to a well-defined intradomain disulfide-bond pattern.[supplied by OMIM, Apr 2004]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.08780643).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SSC4DNM_080744.2 linkc.1023T>G p.Ser341Arg missense_variant, splice_region_variant Exon 9 of 11 ENST00000275560.4 NP_542782.1 Q8WTU2-1
SSC4DXM_024446664.2 linkc.1110T>G p.Ser370Arg missense_variant, splice_region_variant Exon 10 of 12 XP_024302432.1
SSC4DXM_017011750.2 linkc.516T>G p.Ser172Arg missense_variant, splice_region_variant Exon 6 of 8 XP_016867239.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SSC4DENST00000275560.4 linkc.1023T>G p.Ser341Arg missense_variant, splice_region_variant Exon 9 of 11 1 NM_080744.2 ENSP00000275560.3 Q8WTU2-1

Frequencies

GnomAD3 genomes
AF:
0.0000395
AC:
6
AN:
151848
Hom.:
0
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.0000242
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000736
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000624
AC:
1
AN:
16020
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
9314
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
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:
0.000115
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000282
AC:
348
AN:
1235034
Hom.:
0
Cov.:
41
AF XY:
0.000266
AC XY:
160
AN XY:
602484
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000341
Gnomad4 OTH exome
AF:
0.0000789
GnomAD4 genome
AF:
0.0000395
AC:
6
AN:
151848
Hom.:
0
Cov.:
34
AF XY:
0.0000270
AC XY:
2
AN XY:
74172
show subpopulations
Gnomad4 AFR
AF:
0.0000242
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000736
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000142
Hom.:
0
Bravo
AF:
0.0000340
ExAC
AF:
0.0000694
AC:
4

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Oct 26, 2022
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.1023T>G (p.S341R) alteration is located in exon 9 (coding exon 8) of the SSC4D gene. This alteration results from a T to G substitution at nucleotide position 1023, causing the serine (S) at amino acid position 341 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.35
BayesDel_addAF
Benign
-0.31
T
BayesDel_noAF
Benign
-0.47
CADD
Benign
14
DANN
Benign
0.96
DEOGEN2
Benign
0.084
T
Eigen
Benign
-1.1
Eigen_PC
Benign
-1.0
FATHMM_MKL
Benign
0.20
N
LIST_S2
Benign
0.16
T
M_CAP
Uncertain
0.13
D
MetaRNN
Benign
0.088
T
MetaSVM
Benign
-0.99
T
MutationAssessor
Benign
1.5
L
PrimateAI
Pathogenic
0.82
D
PROVEAN
Benign
-1.4
N
REVEL
Benign
0.25
Sift
Uncertain
0.022
D
Sift4G
Benign
0.14
T
Polyphen
0.0
B
Vest4
0.21
MutPred
0.41
Gain of helix (P = 0.0034);
MVP
0.061
MPC
0.64
ClinPred
0.027
T
GERP RS
1.2
Varity_R
0.070
gMVP
0.44

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.0029
dbscSNV1_RF
Benign
0.19
SpliceAI score (max)
0.33
Details are displayed if max score is > 0.2
DS_AL_spliceai
0.33
Position offset: 1

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.

Other links and lift over

dbSNP: rs1198162418; hg19: chr7-76023032; API