chr7-141742852-A-G

Variant names:

• chr7-141742852-A-G
• rs2013816
• NM_003143.3:c.85+623A>G

Variant summary

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

The NM_003143.3(SSBP1):​c.85+623A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 151,988 control chromosomes in the GnomAD database, including 20,463 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 0.52 (20463 hom., cov: 32)
• Consequence: SSBP1 NM_003143.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 13 publications found

Genes affected

SSBP1 (HGNC:11317): (single stranded DNA binding protein 1) SSBP1 is a housekeeping gene involved in mitochondrial biogenesis (Tiranti et al., 1995 [PubMed 7789991]). It is also a subunit of a single-stranded DNA (ssDNA)-binding complex involved in the maintenance of genome stability (Huang et al., 2009) [PubMed 19683501].[supplied by OMIM, Feb 2010]

SSBP1 Gene-Disease associations (from GenCC):

• optic atrophy 13 with retinal and foveal abnormalities

  Inheritance: AD, AR Classification: STRONG, MODERATE, LIMITED Submitted by: PanelApp Australia, ClinGen, Ambry Genetics
• Leigh syndrome

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

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 (EAS) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003143.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSBP1	NM_003143.3	MANE Select	c.85+623A>G		intron	N/A	NP_003134.1	A4D1U3
	SSBP1	NM_001256510.1		c.85+623A>G		intron	N/A	NP_001243439.1	Q04837
	SSBP1	NM_001256511.1		c.85+623A>G		intron	N/A	NP_001243440.1	A4D1U3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSBP1	ENST00000265304.11	TSL:1 MANE Select	c.85+623A>G		intron	N/A	ENSP00000265304.6	Q04837
	SSBP1	ENST00000481508.1	TSL:1	c.85+623A>G		intron	N/A	ENSP00000419665.1	Q04837
	SSBP1	ENST00000498107.5	TSL:1	c.85+623A>G		intron	N/A	ENSP00000419541.1	Q04837

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78570 AN: 151870 Hom.: 20427 Cov.: 32

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.518 AC: 78664 AN: 151988 Hom.: 20463 Cov.: 32 AF XY: 0.521 AC XY: 38687 AN XY: 74294

African (AFR) AF: 0.524 AC: 21743 AN: 41472

American (AMR) AF: 0.547 AC: 8351 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1623 AN: 3466

East Asian (EAS) AF: 0.751 AC: 3873 AN: 5160

South Asian (SAS) AF: 0.594 AC: 2863 AN: 4820

European-Finnish (FIN) AF: 0.487 AC: 5131 AN: 10534

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33575 AN: 67938

Other (OTH) AF: 0.518 AC: 1094 AN: 2112

Alfa AF: 0.501 Hom.: 3468

Bravo AF: 0.525

Asia WGS AF: 0.684 AC: 2376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.36
PhyloP100		0.073
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: rs2013816; hg19: chr7-141442652;