1-113795614-C-T

Variant names:

• chr1-113795614-C-T
• rs1217396
• NM_018364.5:c.1377+1749G>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.1377+1749G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 152,100 control chromosomes in the GnomAD database, including 45,721 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 0.77 (45721 hom., cov: 32)
• Consequence: RSBN1 NM_018364.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.402
• Publications: 15 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RSBN1	NM_018364.5	c.1377+1749G>A		intron_variant	Intron 2 of 6	ENST00000261441.9	NP_060834.2
RSBN1	XM_017001518.3	c.*687G>A		3_prime_UTR_variant	Exon 3 of 3		XP_016857007.1
RSBN1	NR_130896.2	n.1559+572G>A		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RSBN1	ENST00000261441.9	c.1377+1749G>A		intron_variant	Intron 2 of 6	2	NM_018364.5	ENSP00000261441.5
RSBN1	ENST00000612242.4	c.1377+1749G>A		intron_variant	Intron 2 of 6	2		ENSP00000479490.1
RSBN1	ENST00000615321.1	c.1233+1749G>A		intron_variant	Intron 2 of 6	2		ENSP00000480408.1
RSBN1	ENST00000476412.5	n.*115+572G>A		intron_variant	Intron 3 of 7	2		ENSP00000433256.2

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116617 AN: 151982 Hom.: 45667 Cov.: 32

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.767 AC: 116732 AN: 152100 Hom.: 45721 Cov.: 32 AF XY: 0.761 AC XY: 56569 AN XY: 74356

African (AFR) AF: 0.900 AC: 37391 AN: 41536

American (AMR) AF: 0.640 AC: 9781 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2649 AN: 3470

East Asian (EAS) AF: 0.391 AC: 2018 AN: 5164

South Asian (SAS) AF: 0.770 AC: 3709 AN: 4820

European-Finnish (FIN) AF: 0.686 AC: 7234 AN: 10540

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.756 AC: 51421 AN: 67978

Other (OTH) AF: 0.743 AC: 1569 AN: 2112

Alfa AF: 0.752 Hom.: 30120

Bravo AF: 0.762

Asia WGS AF: 0.636 AC: 2212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.33
PhyloP100		0.40
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: rs1217396; hg19: chr1-114338236;