rs10489566

Variant names:

• chr1-54352681-G-C
• rs10489566
• ENST00000610401.6:c.276+49180C>G

Variant summary

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

The ENST00000610401.6(SSBP3):​c.276+49180C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.048 in 152,264 control chromosomes in the GnomAD database, including 333 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 0.048 (333 hom., cov: 32)
• Consequence: SSBP3 ENST00000610401.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302
• Publications: 0 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 = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSBP3	NM_145716.4	c.276+49180C>G		intron_variant	Intron 4 of 17		NP_663768.1
SSBP3	NM_001394360.1	c.276+49180C>G		intron_variant	Intron 4 of 16		NP_001381289.1
SSBP3	NM_018070.5	c.276+49180C>G		intron_variant	Intron 4 of 16		NP_060540.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SSBP3	ENST00000610401.6	c.276+49180C>G		intron_variant	Intron 4 of 17	5		ENSP00000479674.2

Frequencies

GnomAD3 genomes AF: 0.0480 AC: 7309 AN: 152146 Hom.: 334 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0231

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.0458

Gnomad FIN AF: 0.0314

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0166

Gnomad OTH AF: 0.0444

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

GnomAD4 genome AF: 0.0480 AC: 7314 AN: 152264 Hom.: 333 Cov.: 32 AF XY: 0.0475 AC XY: 3538 AN XY: 74452

African (AFR) AF: 0.103 AC: 4287 AN: 41544

American (AMR) AF: 0.0231 AC: 353 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0300 AC: 104 AN: 3470

East Asian (EAS) AF: 0.152 AC: 787 AN: 5166

South Asian (SAS) AF: 0.0465 AC: 224 AN: 4818

European-Finnish (FIN) AF: 0.0314 AC: 333 AN: 10612

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0166 AC: 1130 AN: 68024

Other (OTH) AF: 0.0430 AC: 91 AN: 2116

Alfa AF: 0.0323 Hom.: 32

Bravo AF: 0.0517

Asia WGS AF: 0.0980 AC: 340 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	7.8
DANN	Benign	0.41
PhyloP100		-0.30
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.10		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: rs10489566; hg19: chr1-54818354;