rs3827733

chr1-113795967-A-G

Variant summary

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

The NM_018364.5(RSBN1):c.1377+1396T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,074 control chromosomes in the GnomAD database, including 2,127 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 (2127 hom., cov: 32)
• Consequence: RSBN1 NM_018364.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24

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=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RSBN1	NM_018364.5	c.1377+1396T>C		intron_variant		ENST00000261441.9
RSBN1	XM_017001518.3	c.*334T>C		3_prime_UTR_variant	3/3
RSBN1	NR_130896.2	n.1559+219T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RSBN1	ENST00000261441.9	c.1377+1396T>C		intron_variant		2	NM_018364.5	P1
RSBN1	ENST00000612242.4	c.1377+1396T>C		intron_variant		2		P1
RSBN1	ENST00000615321.1	c.1233+1396T>C		intron_variant		2
RSBN1	ENST00000476412.5	c.*115+219T>C		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23791 AN: 151956 Hom.: 2127 Cov.: 32

Gnomad AFR AF: 0.0819

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.157 AC: 23802 AN: 152074 Hom.: 2127 Cov.: 32 AF XY: 0.157 AC XY: 11701 AN XY: 74354

Gnomad4 AFR AF: 0.0819

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.165

Alfa AF: 0.177 Hom.: 1432

Bravo AF: 0.153

Asia WGS AF: 0.190 AC: 662 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
Cadd	Benign	13
Dann	Benign	0.75

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: rs3827733; hg19: chr1-114338589; COSMIC: COSV54731608;