rs1373965

chr5-81666040-A-Cchr5-81666040-A-T

Variant summary

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

The NM_001256732.3(SSBP2):c.63-15701T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0956 in 152,192 control chromosomes in the GnomAD database, including 1,732 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 0.096 (1732 hom., cov: 32)
• Consequence: SSBP2 NM_001256732.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297

Genes affected

SSBP2 (HGNC:15831): (single stranded DNA binding protein 2) This gene encodes a subunit of a protein complex that interacts with single-stranded DNA and is involved in the DNA damage response and maintenance of genome stability. The encoded protein may also play a role in telomere repair. A variant of this gene may be associated with survival in human glioblastoma patients. [provided by RefSeq, Sep 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SSBP2	NM_001256732.3	c.63-15701T>G		intron_variant		ENST00000615665.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SSBP2	ENST00000615665.5	c.63-15701T>G		intron_variant		5	NM_001256732.3

Frequencies

GnomAD3 genomes AF: 0.0954 AC: 14510 AN: 152074 Hom.: 1729 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0475

Gnomad ASJ AF: 0.0596

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0265

Gnomad FIN AF: 0.0283

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0183

Gnomad OTH AF: 0.0798

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

GnomAD4 genome AF: 0.0956 AC: 14543 AN: 152192 Hom.: 1732 Cov.: 32 AF XY: 0.0934 AC XY: 6952 AN XY: 74408

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.0474

Gnomad4 ASJ AF: 0.0596

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0262

Gnomad4 FIN AF: 0.0283

Gnomad4 NFE AF: 0.0183

Gnomad4 OTH AF: 0.0789

Alfa AF: 0.0222 Hom.: 30

Bravo AF: 0.105

Asia WGS AF: 0.0300 AC: 106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	6.2
Dann	Benign	0.60

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1373965; hg19: chr5-80961859;