rs4145859

Positions:

• chr1-113769813-G-C
• chr1-113769813-G-T

Variant summary

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

The NM_018364.5(RSBN1):​c.1659-1424C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,080 control chromosomes in the GnomAD database, including 3,804 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 0.19 (3804 hom., cov: 32)
• Consequence: RSBN1 NM_018364.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RSBN1	NM_018364.5	c.1659-1424C>G		intron_variant		ENST00000261441.9	NP_060834.2
RSBN1	NR_130896.2	n.1841-1424C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RSBN1	ENST00000261441.9	c.1659-1424C>G		intron_variant		2	NM_018364.5	ENSP00000261441	P1
RSBN1	ENST00000612242.4	c.1659-1424C>G		intron_variant		2		ENSP00000479490	P1
RSBN1	ENST00000615321.1	c.1515-1424C>G		intron_variant		2		ENSP00000480408
RSBN1	ENST00000476412.5	c.*397-1424C>G		intron_variant, NMD_transcript_variant		2		ENSP00000433256

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29153 AN: 151962 Hom.: 3804 Cov.: 32

Gnomad AFR AF: 0.0438

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.192 AC: 29149 AN: 152080 Hom.: 3804 Cov.: 32 AF XY: 0.197 AC XY: 14671 AN XY: 74342

Gnomad4 AFR AF: 0.0436

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.213

Alfa AF: 0.120 Hom.: 242

Bravo AF: 0.191

Asia WGS AF: 0.326 AC: 1132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.63

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: rs4145859; hg19: chr1-114312435; COSMIC: COSV54730828; COSMIC: COSV54730828;