rs1373965

Variant names:

• chr5-81666040-A-C
• rs1373965
• NM_001256732.3:c.63-15701T>G

Your query was ambiguous. Multiple possible variants found:

• chr5-81666040-A-C
• chr5-81666040-A-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.63-15701T>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
• Publications: 1 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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001256732.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSBP2	NM_001256732.3	MANE Select	c.63-15701T>G		intron	N/A	NP_001243661.1
	SSBP2	NM_001394350.1		c.63-15701T>G		intron	N/A	NP_001381279.1
	SSBP2	NM_001400340.1		c.63-15701T>G		intron	N/A	NP_001387269.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSBP2	ENST00000615665.5	TSL:5 MANE Select	c.63-15701T>G		intron	N/A	ENSP00000483921.1
	SSBP2	ENST00000320672.9	TSL:1	c.63-15701T>G		intron	N/A	ENSP00000322977.4
	SSBP2	ENST00000514493.5	TSL:1	c.63-15701T>G		intron	N/A	ENSP00000426183.1

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

African (AFR) AF: 0.283 AC: 11753 AN: 41480

American (AMR) AF: 0.0474 AC: 724 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0596 AC: 207 AN: 3472

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5180

South Asian (SAS) AF: 0.0262 AC: 126 AN: 4818

European-Finnish (FIN) AF: 0.0283 AC: 300 AN: 10602

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0183 AC: 1246 AN: 68030

Other (OTH) AF: 0.0789 AC: 167 AN: 2116

Alfa AF: 0.0325 Hom.: 58

Bravo AF: 0.105

Asia WGS AF: 0.0300 AC: 106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.2
DANN	Benign	0.60
PhyloP100		0.30
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1373965; hg19: chr5-80961859;