1-113812320-T-G

Variant names:

• chr1-113812320-T-G
• rs3789604
• NM_018364.5:c.93A>C

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_018364.5(RSBN1):​c.93A>C​(p.Arg31Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 1,603,660 control chromosomes in the GnomAD database, including 25,635 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 0.16 (2092 hom., cov: 32)
  • Exomes 𝑓: 0.18 (23543 hom.)
• Consequence: RSBN1 NM_018364.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 48 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]

AP4B1-AS1 (HGNC:44114): (AP4B1 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP7: Synonymous conserved (PhyloP=-2 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.218 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RSBN1	NM_018364.5	MANE Select	c.93A>C	p.Arg31Arg	synonymous	Exon 1 of 7	NP_060834.2
	RSBN1	NR_130896.2		n.157A>C		non_coding_transcript_exon	Exon 1 of 8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RSBN1	ENST00000261441.9	TSL:2 MANE Select	c.93A>C	p.Arg31Arg	synonymous	Exon 1 of 7	ENSP00000261441.5	Q5VWQ0-1
	RSBN1	ENST00000612242.4	TSL:2	c.93A>C	p.Arg31Arg	synonymous	Exon 1 of 7	ENSP00000479490.1	Q5VWQ0-1
	RSBN1	ENST00000934566.1		c.93A>C	p.Arg31Arg	synonymous	Exon 1 of 6	ENSP00000604625.1

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23700 AN: 152106 Hom.: 2091 Cov.: 32

Gnomad AFR AF: 0.0815

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.161

GnomAD2 exomes AF: 0.168 AC: 39434 AN: 234336 AF XY: 0.168

Gnomad AFR exome AF: 0.0797

Gnomad AMR exome AF: 0.139

Gnomad ASJ exome AF: 0.154

Gnomad EAS exome AF: 0.231

Gnomad FIN exome AF: 0.190

Gnomad NFE exome AF: 0.192

Gnomad OTH exome AF: 0.169

GnomAD4 exome AF: 0.178 AC: 257862 AN: 1451436 Hom.: 23543 Cov.: 33 AF XY: 0.176 AC XY: 127147 AN XY: 722532

African (AFR) AF: 0.0735 AC: 2459 AN: 33470

American (AMR) AF: 0.141 AC: 6318 AN: 44686

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 4004 AN: 26100

East Asian (EAS) AF: 0.211 AC: 8360 AN: 39678

South Asian (SAS) AF: 0.117 AC: 10065 AN: 86218

European-Finnish (FIN) AF: 0.185 AC: 8051 AN: 43508

Middle Eastern (MID) AF: 0.120 AC: 690 AN: 5768

European-Non Finnish (NFE) AF: 0.187 AC: 207580 AN: 1111696

Other (OTH) AF: 0.171 AC: 10335 AN: 60312

GnomAD4 genome AF: 0.156 AC: 23710 AN: 152224 Hom.: 2092 Cov.: 32 AF XY: 0.157 AC XY: 11669 AN XY: 74424

African (AFR) AF: 0.0816 AC: 3390 AN: 41560

American (AMR) AF: 0.171 AC: 2610 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 536 AN: 3472

East Asian (EAS) AF: 0.229 AC: 1181 AN: 5150

South Asian (SAS) AF: 0.118 AC: 568 AN: 4824

European-Finnish (FIN) AF: 0.198 AC: 2099 AN: 10616

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12735 AN: 67996

Other (OTH) AF: 0.165 AC: 347 AN: 2108

Alfa AF: 0.173 Hom.: 3241

Bravo AF: 0.152

Asia WGS AF: 0.191 AC: 664 AN: 3478

EpiCase AF: 0.180

EpiControl AF: 0.189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.6
DANN	Benign	0.54
PhyloP100		-2.0
PromoterAI		0.073	Neutral
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: rs3789604; hg19: chr1-114354942; COSMIC: COSV54731537; COSMIC: COSV54731537;