NM_001256732.3:c.63-25271G>T

Variant names:

• chr5-81675610-C-A
• rs380946
• NM_001256732.3:c.63-25271G>T

Variant summary

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

The NM_001256732.3(SSBP2):​c.63-25271G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,906 control chromosomes in the GnomAD database, including 11,313 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 0.38 (11313 hom., cov: 32)
• Consequence: SSBP2 NM_001256732.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.603
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSBP2	NM_001256732.3	c.63-25271G>T		intron_variant	Intron 1 of 16	ENST00000615665.5	NP_001243661.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SSBP2	ENST00000615665.5	c.63-25271G>T		intron_variant	Intron 1 of 16	5	NM_001256732.3	ENSP00000483921.1

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57532 AN: 151788 Hom.: 11300 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.0628

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.379 AC: 57586 AN: 151906 Hom.: 11313 Cov.: 32 AF XY: 0.375 AC XY: 27859 AN XY: 74250

African (AFR) AF: 0.425 AC: 17598 AN: 41410

American (AMR) AF: 0.331 AC: 5050 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1816 AN: 3470

East Asian (EAS) AF: 0.0623 AC: 323 AN: 5182

South Asian (SAS) AF: 0.355 AC: 1711 AN: 4816

European-Finnish (FIN) AF: 0.338 AC: 3573 AN: 10558

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26144 AN: 67912

Other (OTH) AF: 0.405 AC: 856 AN: 2112

Alfa AF: 0.361 Hom.: 6829

Bravo AF: 0.379

Asia WGS AF: 0.237 AC: 825 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	0.88
DANN	Benign	0.23
PhyloP100		-0.60
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: rs380946; hg19: chr5-80971429;