rs3927580

Variant names:

• chr1-54319043-A-G
• rs3927580
• ENST00000610401.6:c.277-37516T>C

Variant summary

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

The ENST00000610401.6(SSBP3):​c.277-37516T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 151,966 control chromosomes in the GnomAD database, including 7,396 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 0.30 (7396 hom., cov: 32)
• Consequence: SSBP3 ENST00000610401.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 5 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSBP3	NM_145716.4	c.277-37516T>C		intron_variant	Intron 4 of 17		NP_663768.1
SSBP3	NM_001394360.1	c.277-37516T>C		intron_variant	Intron 4 of 16		NP_001381289.1
SSBP3	NM_018070.5	c.277-37516T>C		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.277-37516T>C		intron_variant	Intron 4 of 17	5		ENSP00000479674.2

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44947 AN: 151848 Hom.: 7373 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.296 AC: 45016 AN: 151966 Hom.: 7396 Cov.: 32 AF XY: 0.298 AC XY: 22157 AN XY: 74286

African (AFR) AF: 0.429 AC: 17782 AN: 41418

American (AMR) AF: 0.295 AC: 4504 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1066 AN: 3472

East Asian (EAS) AF: 0.417 AC: 2140 AN: 5136

South Asian (SAS) AF: 0.343 AC: 1654 AN: 4816

European-Finnish (FIN) AF: 0.241 AC: 2552 AN: 10570

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.213 AC: 14488 AN: 67956

Other (OTH) AF: 0.287 AC: 606 AN: 2108

Alfa AF: 0.243 Hom.: 8193

Bravo AF: 0.309

Asia WGS AF: 0.373 AC: 1296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.061
DANN	Benign	0.17
PhyloP100		-1.8
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: rs3927580; hg19: chr1-54784716;