NM_018364.5:c.704-3425G>A

Variant names:

• chr1-113801461-C-T
• rs1217379
• NM_018364.5:c.704-3425G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018364.5(RSBN1):​c.704-3425G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 151,974 control chromosomes in the GnomAD database, including 25,295 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 0.57 (25295 hom., cov: 32)
• Consequence: RSBN1 NM_018364.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.82
• Publications: 15 publications found

Genes affected

RSBN1 (HGNC:25642): (round spermatid basic protein 1) Predicted to enable dioxygenase activity and metal ion binding activity. Predicted to be involved in chromatin organization. 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018364.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RSBN1	NM_018364.5	MANE Select	c.704-3425G>A		intron	N/A	NP_060834.2
	RSBN1	NR_130896.2		n.768-3425G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RSBN1	ENST00000261441.9	TSL:2 MANE Select	c.704-3425G>A		intron	N/A	ENSP00000261441.5
	RSBN1	ENST00000612242.4	TSL:2	c.704-3425G>A		intron	N/A	ENSP00000479490.1
	RSBN1	ENST00000615321.1	TSL:2	c.560-3425G>A		intron	N/A	ENSP00000480408.1

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86131 AN: 151856 Hom.: 25269 Cov.: 32

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.567 AC: 86210 AN: 151974 Hom.: 25295 Cov.: 32 AF XY: 0.561 AC XY: 41692 AN XY: 74254

African (AFR) AF: 0.664 AC: 27532 AN: 41444

American (AMR) AF: 0.454 AC: 6930 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2122 AN: 3470

East Asian (EAS) AF: 0.160 AC: 829 AN: 5176

South Asian (SAS) AF: 0.649 AC: 3133 AN: 4824

European-Finnish (FIN) AF: 0.489 AC: 5155 AN: 10546

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38648 AN: 67946

Other (OTH) AF: 0.547 AC: 1154 AN: 2110

Alfa AF: 0.570 Hom.: 30928

Bravo AF: 0.560

Asia WGS AF: 0.437 AC: 1521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	14
DANN	Benign	0.42
PhyloP100		1.8
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: rs1217379; hg19: chr1-114344083;