7-141762737-G-T

Position:

• chr7-141762737-G-T

Variant summary

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

The ENST00000465582.5(SSBP1):​c.*30+12353G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 152,188 control chromosomes in the GnomAD database, including 14,414 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 0.42 (14414 hom., cov: 34)
• Consequence: SSBP1 ENST00000465582.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.767

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.141762737G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SSBP1	ENST00000465582.5	c.*30+12353G>T		intron_variant		5		ENSP00000420485.1

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63841 AN: 152070 Hom.: 14407 Cov.: 34

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.420 AC: 63877 AN: 152188 Hom.: 14414 Cov.: 34 AF XY: 0.422 AC XY: 31428 AN XY: 74410

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.686

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.455

Alfa AF: 0.425 Hom.: 4564

Bravo AF: 0.416

Asia WGS AF: 0.552 AC: 1917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.32
DANN	Benign	0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11763979; hg19: chr7-141462537;