7-141744038-G-A

Position:

• chr7-141744038-G-A

Variant summary

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

The NM_003143.3(SSBP1):​c.314+49G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0116 in 1,522,404 control chromosomes in the GnomAD database, including 1,751 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 0.061 (964 hom., cov: 33)
  • Exomes 𝑓: 0.0062 (787 hom.)
• Consequence: SSBP1 NM_003143.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SSBP1	NM_003143.3	c.314+49G>A		intron_variant		ENST00000265304.11	NP_003134.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SSBP1	ENST00000265304.11	c.314+49G>A		intron_variant		1	NM_003143.3	ENSP00000265304	P1

Frequencies

GnomAD3 genomes AF: 0.0607 AC: 9231 AN: 152122 Hom.: 959 Cov.: 33

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0237

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00124

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.000573

Gnomad OTH AF: 0.0397

GnomAD3 exomes AF: 0.0171 AC: 3754 AN: 219404 Hom.: 374 AF XY: 0.0124 AC XY: 1471 AN XY: 118656

Gnomad AFR exome AF: 0.220

Gnomad AMR exome AF: 0.0107

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000567

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000455

Gnomad OTH exome AF: 0.00887

GnomAD4 exome AF: 0.00616 AC: 8438 AN: 1370166 Hom.: 787 Cov.: 20 AF XY: 0.00525 AC XY: 3592 AN XY: 684478

Gnomad4 AFR exome AF: 0.218

Gnomad4 AMR exome AF: 0.0120

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000332

Gnomad4 SAS exome AF: 0.000629

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000286

Gnomad4 OTH exome AF: 0.0145

GnomAD4 genome AF: 0.0608 AC: 9262 AN: 152238 Hom.: 964 Cov.: 33 AF XY: 0.0588 AC XY: 4377 AN XY: 74454

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.0237

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00104

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000573

Gnomad4 OTH AF: 0.0393

Alfa AF: 0.00734 Hom.: 69

Bravo AF: 0.0706

Asia WGS AF: 0.0140 AC: 48 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.0
DANN	Benign	0.68

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

Publications

LitVar

Other links and lift over

dbSNP: rs6957284; hg19: chr7-141443838;