chr1-54356942-C-G

Position:

• chr1-54356942-C-G

Variant summary

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

The ENST00000610401.6(SSBP3):​c.276+44919G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,320 control chromosomes in the GnomAD database, including 1,745 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 0.12 (1742 hom., cov: 32)
  • Exomes 𝑓: 0.20 (3 hom.)
• Consequence: SSBP3 ENST00000610401.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SSBP3	NM_145716.4	c.276+44919G>C		intron_variant		ENST00000610401.6	NP_663768.1
SSBP3	NM_001394365.1	c.-55+56414G>C		intron_variant			NP_001381294.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SSBP3	ENST00000610401.6	c.276+44919G>C		intron_variant		5	NM_145716.4	ENSP00000479674	P1

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18840 AN: 152128 Hom.: 1737 Cov.: 32

Gnomad AFR AF: 0.0284

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.0815

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.138

GnomAD4 exome AF: 0.203 AC: 15 AN: 74 Hom.: 3 AF XY: 0.220 AC XY: 11 AN XY: 50

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.227

GnomAD4 genome AF: 0.124 AC: 18846 AN: 152246 Hom.: 1742 Cov.: 32 AF XY: 0.128 AC XY: 9515 AN XY: 74424

Gnomad4 AFR AF: 0.0283

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.0815

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.142

Alfa AF: 0.132 Hom.: 187

Bravo AF: 0.119

Asia WGS AF: 0.355 AC: 1233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.1
DANN	Benign	0.38

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: rs4927095; hg19: chr1-54822615; COSMIC: COSV58885540; COSMIC: COSV58885540;