1-54277735-G-A

Position:

• chr1-54277735-G-A

Variant summary

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

The NM_001394365.1(SSBP3):​c.36+3703C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,110 control chromosomes in the GnomAD database, including 2,188 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 0.17 (2188 hom., cov: 32)
• Consequence: SSBP3 NM_001394365.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SSBP3	NM_145716.4	c.366+3703C>T		intron_variant		ENST00000610401.6	NP_663768.1
SSBP3	NM_001394365.1	c.36+3703C>T		intron_variant			NP_001381294.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SSBP3	ENST00000610401.6	c.366+3703C>T		intron_variant		5	NM_145716.4	ENSP00000479674	P1

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25174 AN: 151992 Hom.: 2185 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.176

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.166 AC: 25196 AN: 152110 Hom.: 2188 Cov.: 32 AF XY: 0.166 AC XY: 12351 AN XY: 74346

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.176

Alfa AF: 0.157 Hom.: 2650

Bravo AF: 0.166

Asia WGS AF: 0.214 AC: 746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.0
DANN	Benign	0.46

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: rs11206315; hg19: chr1-54743408;