rs6697414

chr1-54289418-C-A

Variant summary

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

The ENST00000610401.6(SSBP3):c.277-7891G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 151,074 control chromosomes in the GnomAD database, including 11,006 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 0.36 (11006 hom., cov: 29)
• Consequence: SSBP3 ENST00000610401.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

Genes affected

SSBP3 (HGNC:15674): (single stranded DNA binding protein 3) Predicted to enable single-stranded DNA binding activity and transcription coactivator activity. Predicted to be involved in head development and positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within hematopoietic progenitor cell differentiation. Predicted to be part of protein-containing complex. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SSBP3	NM_145716.4	c.277-7891G>T		intron_variant		ENST00000610401.6
SSBP3	NM_001394365.1	c.-54-7891G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SSBP3	ENST00000610401.6	c.277-7891G>T		intron_variant		5	NM_145716.4	P1

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54191 AN: 150956 Hom.: 10977 Cov.: 29

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.359 AC: 54279 AN: 151074 Hom.: 11006 Cov.: 29 AF XY: 0.362 AC XY: 26724 AN XY: 73740

Gnomad4 AFR AF: 0.535

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.513

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.364

Alfa AF: 0.298 Hom.: 9411

Bravo AF: 0.373

Asia WGS AF: 0.417 AC: 1451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.021
Dann	Benign	0.40

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: rs6697414; hg19: chr1-54755091; COSMIC: COSV58885391; COSMIC: COSV58885391;