NM_018364.5:c.1377+234T>C

Variant names:

• chr1-113797129-A-G
• rs3789602
• NM_018364.5:c.1377+234T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_018364.5(RSBN1):​c.1377+234T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0204 in 152,316 control chromosomes in the GnomAD database, including 48 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 0.020 (48 hom., cov: 32)
• Consequence: RSBN1 NM_018364.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29
• Publications: 4 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=-0.83).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0204 (3113/152316) while in subpopulation NFE AF = 0.0298 (2027/68020). AF 95% confidence interval is 0.0287. There are 48 homozygotes in GnomAd4. There are 1461 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High AC in GnomAd4 at 3113 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RSBN1	NM_018364.5	c.1377+234T>C		intron_variant	Intron 2 of 6	ENST00000261441.9	NP_060834.2
RSBN1	NR_130896.2	n.1441+234T>C		intron_variant	Intron 2 of 7
RSBN1	XM_017001518.3	c.1377+234T>C		intron_variant	Intron 2 of 2		XP_016857007.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RSBN1	ENST00000261441.9	c.1377+234T>C		intron_variant	Intron 2 of 6	2	NM_018364.5	ENSP00000261441.5
RSBN1	ENST00000612242.4	c.1377+234T>C		intron_variant	Intron 2 of 6	2		ENSP00000479490.1
RSBN1	ENST00000615321.1	c.1233+234T>C		intron_variant	Intron 2 of 6	2		ENSP00000480408.1
RSBN1	ENST00000476412.5	n.1233+234T>C		intron_variant	Intron 2 of 7	2		ENSP00000433256.2

Frequencies

GnomAD3 genomes AF: 0.0204 AC: 3111 AN: 152198 Hom.: 48 Cov.: 32

Gnomad AFR AF: 0.00555

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0152

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.0158

Gnomad SAS AF: 0.0242

Gnomad FIN AF: 0.0246

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0298

Gnomad OTH AF: 0.0191

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

GnomAD4 genome AF: 0.0204 AC: 3113 AN: 152316 Hom.: 48 Cov.: 32 AF XY: 0.0196 AC XY: 1461 AN XY: 74472

African (AFR) AF: 0.00553 AC: 230 AN: 41574

American (AMR) AF: 0.0152 AC: 232 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0314 AC: 109 AN: 3472

East Asian (EAS) AF: 0.0158 AC: 82 AN: 5194

South Asian (SAS) AF: 0.0245 AC: 118 AN: 4826

European-Finnish (FIN) AF: 0.0246 AC: 261 AN: 10616

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0298 AC: 2027 AN: 68020

Other (OTH) AF: 0.0189 AC: 40 AN: 2116

Alfa AF: 0.0282 Hom.: 164

Bravo AF: 0.0195

Asia WGS AF: 0.0180 AC: 64 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.4
DANN	Benign	0.67
PhyloP100		1.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=100/0	polymorphism

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: rs3789602; hg19: chr1-114339751;