rs213498

Variant names:

• chr1-54401501-T-A
• rs213498
• NM_145716.4:c.276+360A>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_145716.4(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 NM_145716.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145716.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSBP3	NM_145716.4	MANE Select	c.276+360A>T		intron	N/A	NP_663768.1
	SSBP3	NM_001394360.1		c.276+360A>T		intron	N/A	NP_001381289.1
	SSBP3	NM_018070.5		c.276+360A>T		intron	N/A	NP_060540.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSBP3	ENST00000610401.6	TSL:5 MANE Select	c.276+360A>T		intron	N/A	ENSP00000479674.2
	SSBP3	ENST00000357475.9	TSL:1	c.276+360A>T		intron	N/A	ENSP00000350067.4
	SSBP3	ENST00000371320.8	TSL:1	n.549+360A>T		intron	N/A

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

African (AFR) AF: 0.388 AC: 16082 AN: 41430

American (AMR) AF: 0.323 AC: 4936 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1813 AN: 3472

East Asian (EAS) AF: 0.460 AC: 2381 AN: 5178

South Asian (SAS) AF: 0.294 AC: 1415 AN: 4816

European-Finnish (FIN) AF: 0.324 AC: 3428 AN: 10568

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22669 AN: 67994

Other (OTH) AF: 0.363 AC: 768 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.17
DANN	Benign	0.72
PhyloP100		-0.76
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs213498; hg19: chr1-54867174;