rs6668829

chr1-113787831-C-T

Variant summary

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

The NM_018364.5(RSBN1):c.1377+9532G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,144 control chromosomes in the GnomAD database, including 4,495 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 0.22 (4495 hom., cov: 32)
• Consequence: RSBN1 NM_018364.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.354

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RSBN1	NM_018364.5	c.1377+9532G>A		intron_variant		ENST00000261441.9
RSBN1	XM_017001518.3	c.*8470G>A		3_prime_UTR_variant	3/3
RSBN1	NR_130896.2	n.1559+8355G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RSBN1	ENST00000261441.9	c.1377+9532G>A		intron_variant		2	NM_018364.5	P1
RSBN1	ENST00000612242.4	c.1377+9532G>A		intron_variant		2		P1
RSBN1	ENST00000615321.1	c.1233+9532G>A		intron_variant		2
RSBN1	ENST00000476412.5	c.*115+8355G>A		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.217 AC: 33027 AN: 152026 Hom.: 4496 Cov.: 32

Gnomad AFR AF: 0.0594

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.0920

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.217 AC: 33035 AN: 152144 Hom.: 4495 Cov.: 32 AF XY: 0.218 AC XY: 16189 AN XY: 74358

Gnomad4 AFR AF: 0.0593

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.0921

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.245

Alfa AF: 0.255 Hom.: 1464

Bravo AF: 0.206

Asia WGS AF: 0.238 AC: 827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.1
Dann	Benign	0.69

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: rs6668829; hg19: chr1-114330453;