rs12144309

Variant names:

• chr1-113772871-C-T
• rs12144309
• NM_018364.5:c.1658+4339G>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.1658+4339G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,052 control chromosomes in the GnomAD database, including 2,749 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 0.18 (2749 hom., cov: 32)
• Consequence: RSBN1 NM_018364.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193
• Publications: 13 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=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RSBN1	NM_018364.5	c.1658+4339G>A		intron_variant	Intron 4 of 6	ENST00000261441.9	NP_060834.2
RSBN1	NR_130896.2	n.1840+4339G>A		intron_variant	Intron 5 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RSBN1	ENST00000261441.9	c.1658+4339G>A		intron_variant	Intron 4 of 6	2	NM_018364.5	ENSP00000261441.5
RSBN1	ENST00000612242.4	c.1658+4339G>A		intron_variant	Intron 4 of 6	2		ENSP00000479490.1
RSBN1	ENST00000615321.1	c.1514+4339G>A		intron_variant	Intron 4 of 6	2		ENSP00000480408.1
RSBN1	ENST00000476412.5	n.*396+4339G>A		intron_variant	Intron 5 of 7	2		ENSP00000433256.2

Frequencies

GnomAD3 genomes AF: 0.184 AC: 28000 AN: 151934 Hom.: 2744 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.0306

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.184 AC: 28009 AN: 152052 Hom.: 2749 Cov.: 32 AF XY: 0.182 AC XY: 13498 AN XY: 74346

African (AFR) AF: 0.208 AC: 8637 AN: 41464

American (AMR) AF: 0.130 AC: 1980 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 832 AN: 3470

East Asian (EAS) AF: 0.0307 AC: 159 AN: 5184

South Asian (SAS) AF: 0.217 AC: 1048 AN: 4826

European-Finnish (FIN) AF: 0.149 AC: 1569 AN: 10562

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13163 AN: 67954

Other (OTH) AF: 0.160 AC: 338 AN: 2110

Alfa AF: 0.184 Hom.: 3483

Bravo AF: 0.177

Asia WGS AF: 0.116 AC: 404 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	6.5
DANN	Benign	0.81
PhyloP100		-0.19
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: rs12144309; hg19: chr1-114315493;