rs3789602

Positions:

• chr1-113797129-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_018364.5(RSBN1):​c.1377+234T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0204 in 152,316 control chromosomes in the GnomAD database, including 48 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 0.020 (48 hom., cov: 32)
• Consequence: RSBN1 NM_018364.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29

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=-0.83).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0204 (3113/152316) while in subpopulation NFE AF= 0.0298 (2027/68020). AF 95% confidence interval is 0.0287. There are 48 homozygotes in gnomad4. There are 1461 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 3113 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RSBN1	NM_018364.5	c.1377+234T>C		intron_variant		ENST00000261441.9	NP_060834.2
RSBN1	XM_017001518.3	c.1377+234T>C		intron_variant			XP_016857007.1
RSBN1	NR_130896.2	n.1441+234T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RSBN1	ENST00000261441.9	c.1377+234T>C		intron_variant		2	NM_018364.5	ENSP00000261441	P1
RSBN1	ENST00000612242.4	c.1377+234T>C		intron_variant		2		ENSP00000479490	P1
RSBN1	ENST00000615321.1	c.1233+234T>C		intron_variant		2		ENSP00000480408
RSBN1	ENST00000476412.5	c.1233+234T>C		intron_variant, NMD_transcript_variant		2		ENSP00000433256

Frequencies

GnomAD3 genomes AF: 0.0204 AC: 3111 AN: 152198 Hom.: 48 Cov.: 32

Gnomad AFR AF: 0.00555

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0152

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.0158

Gnomad SAS AF: 0.0242

Gnomad FIN AF: 0.0246

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0298

Gnomad OTH AF: 0.0191

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

GnomAD4 genome AF: 0.0204 AC: 3113 AN: 152316 Hom.: 48 Cov.: 32 AF XY: 0.0196 AC XY: 1461 AN XY: 74472

Gnomad4 AFR AF: 0.00553

Gnomad4 AMR AF: 0.0152

Gnomad4 ASJ AF: 0.0314

Gnomad4 EAS AF: 0.0158

Gnomad4 SAS AF: 0.0245

Gnomad4 FIN AF: 0.0246

Gnomad4 NFE AF: 0.0298

Gnomad4 OTH AF: 0.0189

Alfa AF: 0.0275 Hom.: 57

Bravo AF: 0.0195

Asia WGS AF: 0.0180 AC: 64 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.4
DANN	Benign	0.67
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs3789602; hg19: chr1-114339751;