NM_145716.4:c.276+4864C>G

Variant names:

• chr1-54396997-G-C
• rs213501
• NM_145716.4:c.276+4864C>G

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+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 NM_145716.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48
• Publications: 1 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.699 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+4864C>G		intron	N/A	NP_663768.1
	SSBP3	NM_001394360.1		c.276+4864C>G		intron	N/A	NP_001381289.1
	SSBP3	NM_018070.5		c.276+4864C>G		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+4864C>G		intron	N/A	ENSP00000479674.2
	SSBP3	ENST00000357475.9	TSL:1	c.276+4864C>G		intron	N/A	ENSP00000350067.4
	SSBP3	ENST00000371320.8	TSL:1	n.549+4864C>G		intron	N/A

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

African (AFR) AF: 0.705 AC: 29255 AN: 41480

American (AMR) AF: 0.368 AC: 5632 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1910 AN: 3460

East Asian (EAS) AF: 0.537 AC: 2767 AN: 5156

South Asian (SAS) AF: 0.349 AC: 1681 AN: 4818

European-Finnish (FIN) AF: 0.376 AC: 3987 AN: 10590

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24156 AN: 67976

Other (OTH) AF: 0.453 AC: 956 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	13
DANN	Benign	0.50
PhyloP100		1.5
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: rs213501; hg19: chr1-54862670;