rs646534

Positions:

• chr1-54269065-G-A
• chr1-54269065-G-C

Variant summary

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

The ENST00000610401.6(SSBP3):​c.367-10916C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,926 control chromosomes in the GnomAD database, including 13,019 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 0.41 (13019 hom., cov: 32)
• Consequence: SSBP3 ENST00000610401.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426

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 (SAS) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SSBP3	NM_145716.4	c.367-10916C>T		intron_variant		ENST00000610401.6
SSBP3	NM_001394365.1	c.37-11879C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SSBP3	ENST00000610401.6	c.367-10916C>T		intron_variant		5	NM_145716.4	P1

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62431 AN: 151808 Hom.: 13006 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.411 AC: 62492 AN: 151926 Hom.: 13019 Cov.: 32 AF XY: 0.408 AC XY: 30268 AN XY: 74262

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.482

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.398

Alfa AF: 0.340 Hom.: 1445

Bravo AF: 0.404

Asia WGS AF: 0.409 AC: 1424 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	0.64
DANN	Benign	0.62

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: rs646534; hg19: chr1-54734738;