rs7732320

Variant names:

• chr5-81423306-C-T
• rs7732320
• NM_001256732.3:c.1081-2773G>A

Variant summary

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

The NM_001256732.3(SSBP2):​c.1081-2773G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,040 control chromosomes in the GnomAD database, including 5,109 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 0.21 (5109 hom., cov: 32)
• Consequence: SSBP2 NM_001256732.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264
• Publications: 12 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSBP2	NM_001256732.3	c.1081-2773G>A		intron_variant	Intron 16 of 16	ENST00000615665.5	NP_001243661.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SSBP2	ENST00000615665.5	c.1081-2773G>A		intron_variant	Intron 16 of 16	5	NM_001256732.3	ENSP00000483921.1

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31816 AN: 151922 Hom.: 5090 Cov.: 32

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.0793

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.210 AC: 31888 AN: 152040 Hom.: 5109 Cov.: 32 AF XY: 0.207 AC XY: 15354 AN XY: 74328

African (AFR) AF: 0.454 AC: 18809 AN: 41452

American (AMR) AF: 0.147 AC: 2241 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 560 AN: 3466

East Asian (EAS) AF: 0.0795 AC: 411 AN: 5170

South Asian (SAS) AF: 0.129 AC: 622 AN: 4818

European-Finnish (FIN) AF: 0.115 AC: 1216 AN: 10546

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.110 AC: 7473 AN: 67990

Other (OTH) AF: 0.181 AC: 381 AN: 2110

Alfa AF: 0.141 Hom.: 8953

Bravo AF: 0.224

Asia WGS AF: 0.123 AC: 427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.41
PhyloP100		-0.26
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: rs7732320; hg19: chr5-80719125;