rs4061073

Positions:

• chr1-54231070-A-G
• chr1-54231070-A-T

Variant summary

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

The ENST00000610401.6(SSBP3):​c.928-2244T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,136 control chromosomes in the GnomAD database, including 5,903 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 0.28 (5903 hom., cov: 32)
• Consequence: SSBP3 ENST00000610401.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SSBP3	NM_145716.4	c.928-2244T>C		intron_variant		ENST00000610401.6
SSBP3	NM_001394365.1	c.517-2244T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SSBP3	ENST00000610401.6	c.928-2244T>C		intron_variant		5	NM_145716.4	P1

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41900 AN: 152018 Hom.: 5900 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.275 AC: 41910 AN: 152136 Hom.: 5903 Cov.: 32 AF XY: 0.269 AC XY: 20042 AN XY: 74372

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.245

Alfa AF: 0.285 Hom.: 5103

Bravo AF: 0.273

Asia WGS AF: 0.226 AC: 789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.64
DANN	Benign	0.21

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: rs4061073; hg19: chr1-54696743;