rs6537798

Variant names:

• chr1-113809084-C-A
• rs6537798
• NM_018364.5:c.703+2626G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-113809084-C-A
• chr1-113809084-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018364.5(RSBN1):​c.703+2626G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 151,554 control chromosomes in the GnomAD database, including 24,267 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 0.56 (24267 hom., cov: 31)
• Consequence: RSBN1 NM_018364.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128
• Publications: 16 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=-0.68).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RSBN1	NM_018364.5	c.703+2626G>T		intron_variant	Intron 1 of 6	ENST00000261441.9	NP_060834.2
RSBN1	NR_130896.2	n.767+2626G>T		intron_variant	Intron 1 of 7
RSBN1	XM_017001518.3	c.703+2626G>T		intron_variant	Intron 1 of 2		XP_016857007.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RSBN1	ENST00000261441.9	c.703+2626G>T		intron_variant	Intron 1 of 6	2	NM_018364.5	ENSP00000261441.5
RSBN1	ENST00000612242.4	c.703+2626G>T		intron_variant	Intron 1 of 6	2		ENSP00000479490.1
RSBN1	ENST00000615321.1	c.559+2626G>T		intron_variant	Intron 1 of 6	2		ENSP00000480408.1
RSBN1	ENST00000476412.5	n.559+2626G>T		intron_variant	Intron 1 of 7	2		ENSP00000433256.2

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84453 AN: 151444 Hom.: 24244 Cov.: 31

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.558 AC: 84524 AN: 151554 Hom.: 24267 Cov.: 31 AF XY: 0.552 AC XY: 40877 AN XY: 74008

African (AFR) AF: 0.628 AC: 25972 AN: 41340

American (AMR) AF: 0.452 AC: 6886 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2122 AN: 3470

East Asian (EAS) AF: 0.161 AC: 831 AN: 5150

South Asian (SAS) AF: 0.652 AC: 3131 AN: 4802

European-Finnish (FIN) AF: 0.492 AC: 5119 AN: 10410

Middle Eastern (MID) AF: 0.603 AC: 175 AN: 290

European-Non Finnish (NFE) AF: 0.569 AC: 38619 AN: 67862

Other (OTH) AF: 0.541 AC: 1134 AN: 2096

Alfa AF: 0.554 Hom.: 30111

Bravo AF: 0.549

Asia WGS AF: 0.434 AC: 1507 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	4.1
DANN	Benign	0.74
PhyloP100		0.13
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: rs6537798; hg19: chr1-114351706;