rs1217379

chr1-113801461-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RSBN1	NM_018364.5	c.704-3425G>A		intron_variant		ENST00000261441.9
RSBN1	XM_017001518.3	c.704-3425G>A		intron_variant
RSBN1	NR_130896.2	n.768-3425G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RSBN1	ENST00000261441.9	c.704-3425G>A		intron_variant		2	NM_018364.5	P1
RSBN1	ENST00000612242.4	c.704-3425G>A		intron_variant		2		P1
RSBN1	ENST00000615321.1	c.560-3425G>A		intron_variant		2
RSBN1	ENST00000476412.5	c.560-3425G>A		intron_variant, NMD_transcript_variant		2

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

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.547

Alfa AF: 0.570 Hom.: 23343

Bravo AF: 0.560

Asia WGS AF: 0.437 AC: 1521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	14
Dann	Benign	0.42

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: rs1217379; hg19: chr1-114344083;