chr1-54289418-C-A

Variant names:

• chr1-54289418-C-A
• rs6697414
• ENST00000610401.6:c.277-7891G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SSBP3	NM_145716.4	c.277-7891G>T		intron_variant	Intron 4 of 17		NP_663768.1
SSBP3	NM_001394360.1	c.277-7891G>T		intron_variant	Intron 4 of 16		NP_001381289.1
SSBP3	NM_018070.5	c.277-7891G>T		intron_variant	Intron 4 of 16		NP_060540.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SSBP3	ENST00000610401.6	c.277-7891G>T		intron_variant	Intron 4 of 17	5		ENSP00000479674.2

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

African (AFR) AF: 0.535 AC: 21925 AN: 40998

American (AMR) AF: 0.394 AC: 5981 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1107 AN: 3470

East Asian (EAS) AF: 0.153 AC: 780 AN: 5084

South Asian (SAS) AF: 0.513 AC: 2437 AN: 4754

European-Finnish (FIN) AF: 0.252 AC: 2628 AN: 10422

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18271 AN: 67854

Other (OTH) AF: 0.364 AC: 766 AN: 2104

Alfa AF: 0.307 Hom.: 14142

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
PhyloP100		-1.7
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: rs6697414; hg19: chr1-54755091; COSMIC: COSV58885391; COSMIC: COSV58885391;