rs213498

Positions:

• chr1-54401501-T-A
• chr1-54401501-T-C

Variant summary

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

The ENST00000610401.6(SSBP3):​c.276+360A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 152,066 control chromosomes in the GnomAD database, including 9,760 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 0.35 (9760 hom., cov: 32)
• Consequence: SSBP3 ENST00000610401.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SSBP3	NM_145716.4	c.276+360A>T		intron_variant		ENST00000610401.6	NP_663768.1
SSBP3	NM_001394365.1	c.-55+11855A>T		intron_variant			NP_001381294.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SSBP3	ENST00000610401.6	c.276+360A>T		intron_variant		5	NM_145716.4	ENSP00000479674	P1

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53869 AN: 151948 Hom.: 9755 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.355 AC: 53910 AN: 152066 Hom.: 9760 Cov.: 32 AF XY: 0.354 AC XY: 26290 AN XY: 74352

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.363

Alfa AF: 0.185 Hom.: 365

Bravo AF: 0.357

Asia WGS AF: 0.361 AC: 1255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.17
DANN	Benign	0.72

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: rs213498; hg19: chr1-54867174;