rs2797409

Positions:

• chr1-113787580-T-C

Variant summary

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

The NM_018364.5(RSBN1):​c.1378-9772A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 151,982 control chromosomes in the GnomAD database, including 6,339 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 0.28 (6339 hom., cov: 32)
• Consequence: RSBN1 NM_018364.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RSBN1	NM_018364.5	c.1378-9772A>G		intron_variant		ENST00000261441.9	NP_060834.2
RSBN1	XM_017001518.3	c.*8721A>G		3_prime_UTR_variant	3/3		XP_016857007.1
RSBN1	NR_130896.2	n.1559+8606A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RSBN1	ENST00000261441.9	c.1378-9772A>G		intron_variant		2	NM_018364.5	ENSP00000261441	P1
RSBN1	ENST00000612242.4	c.1378-9772A>G		intron_variant		2		ENSP00000479490	P1
RSBN1	ENST00000615321.1	c.1234-9772A>G		intron_variant		2		ENSP00000480408
RSBN1	ENST00000476412.5	c.*115+8606A>G		intron_variant, NMD_transcript_variant		2		ENSP00000433256

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42221 AN: 151864 Hom.: 6334 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.278 AC: 42250 AN: 151982 Hom.: 6339 Cov.: 32 AF XY: 0.283 AC XY: 21016 AN XY: 74272

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.289

Alfa AF: 0.256 Hom.: 7337

Bravo AF: 0.288

Asia WGS AF: 0.372 AC: 1291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.1
DANN	Benign	0.81

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: rs2797409; hg19: chr1-114330202;