1-54243284-T-C

Variant names:

• chr1-54243284-T-C
• ENST00000610401.6:c.667A>G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_145716.4(SSBP3):​c.667A>G​(p.Met223Val) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: SSBP3 NM_145716.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 5.62

Genes affected

SSBP3 (HGNC:15674): (single stranded DNA binding protein 3) Predicted to enable single-stranded DNA binding activity and transcription coactivator activity. Predicted to be involved in head development and positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within hematopoietic progenitor cell differentiation. Predicted to be part of protein-containing complex. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSBP3	NM_145716.4	c.667A>G	p.Met223Val	missense_variant	Exon 10 of 18		NP_663768.1
SSBP3	NM_001394360.1	c.610A>G	p.Met204Val	missense_variant	Exon 9 of 17		NP_001381289.1
SSBP3	NM_018070.5	c.607A>G	p.Met203Val	missense_variant	Exon 9 of 17		NP_060540.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SSBP3	ENST00000610401.6	c.667A>G	p.Met223Val	missense_variant	Exon 10 of 18	5		ENSP00000479674.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Jan 09, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.667A>G (p.M223V) alteration is located in exon 10 (coding exon 10) of the SSBP3 gene. This alteration results from a A to G substitution at nucleotide position 667, causing the methionine (M) at amino acid position 223 to be replaced by a valine (V). 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	Benign	0.15
BayesDel_addAF	Pathogenic	0.27	D
BayesDel_noAF	Pathogenic	0.15
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Benign	0.12	T;.;D;.;.;.;.
Eigen	Uncertain	0.23
Eigen_PC	Uncertain	0.26
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.94	D;D;D;D;D;D;D
M_CAP	Benign	0.011	T
MetaRNN	Uncertain	0.69	D;D;D;D;D;D;D
MetaSVM	Benign	-0.50	T
MutationAssessor	Uncertain	2.6	.;.;M;.;.;.;.
PrimateAI	Uncertain	0.72	T
PROVEAN	Uncertain	-3.1	.;D;D;D;D;D;D
REVEL	Pathogenic	0.73
Sift	Uncertain	0.0020	.;D;D;D;D;D;D
Sift4G	Benign	0.34	T;T;T;T;T;T;D
Polyphen		0.74, 0.92, 0.065	.;.;P;P;B;.;.
Vest4		0.72, 0.80, 0.76, 0.79
MutPred		0.59		.;.;Loss of glycosylation at P225 (P = 0.1161);.;.;.;.;
MVP		0.44
MPC		1.0
ClinPred		0.95	D
GERP RS		3.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.56
gMVP		0.58

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-54708957;