rs213501

Positions:

• chr1-54396997-G-C
• chr1-54396997-G-T

Variant summary

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

The ENST00000610401.6(SSBP3):​c.276+4864C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 152,082 control chromosomes in the GnomAD database, including 18,301 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 0.47 (18301 hom., cov: 33)
• Consequence: SSBP3 ENST00000610401.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SSBP3	NM_145716.4	c.276+4864C>G		intron_variant		ENST00000610401.6	NP_663768.1
SSBP3	NM_001394365.1	c.-55+16359C>G		intron_variant			NP_001381294.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SSBP3	ENST00000610401.6	c.276+4864C>G		intron_variant		5	NM_145716.4	ENSP00000479674	P1

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70694 AN: 151964 Hom.: 18275 Cov.: 33

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.465 AC: 70776 AN: 152082 Hom.: 18301 Cov.: 33 AF XY: 0.463 AC XY: 34429 AN XY: 74356

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.453

Alfa AF: 0.399 Hom.: 1603

Bravo AF: 0.478

Asia WGS AF: 0.433 AC: 1505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	13
DANN	Benign	0.50

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: rs213501; hg19: chr1-54862670;