NM_198467.3:c.587-362T>C

Variant names:

• chr7-77736048-T-C
• rs10488040
• NM_198467.3:c.587-362T>C

Variant summary

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

The NM_198467.3(RSBN1L):​c.587-362T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 151,974 control chromosomes in the GnomAD database, including 14,200 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 0.43 (14200 hom., cov: 32)
• Consequence: RSBN1L NM_198467.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36
• Publications: 4 publications found

Genes affected

RSBN1L (HGNC:24765): (round spermatid basic protein 1 like) Predicted to enable dioxygenase activity and metal ion binding activity. 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RSBN1L	NM_198467.3	c.587-362T>C		intron_variant	Intron 1 of 7	ENST00000334955.13	NP_940869.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RSBN1L	ENST00000334955.13	c.587-362T>C		intron_variant	Intron 1 of 7	1	NM_198467.3	ENSP00000334040.7
RSBN1L	ENST00000445288.5	c.-224-362T>C		intron_variant	Intron 1 of 7	5		ENSP00000393888.1

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64664 AN: 151856 Hom.: 14172 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.426 AC: 64753 AN: 151974 Hom.: 14200 Cov.: 32 AF XY: 0.420 AC XY: 31199 AN XY: 74286

African (AFR) AF: 0.505 AC: 20921 AN: 41462

American (AMR) AF: 0.378 AC: 5775 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1712 AN: 3470

East Asian (EAS) AF: 0.201 AC: 1039 AN: 5180

South Asian (SAS) AF: 0.359 AC: 1729 AN: 4814

European-Finnish (FIN) AF: 0.363 AC: 3830 AN: 10564

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28259 AN: 67902

Other (OTH) AF: 0.423 AC: 894 AN: 2112

Alfa AF: 0.392 Hom.: 5965

Bravo AF: 0.425

Asia WGS AF: 0.346 AC: 1201 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.046
DANN	Benign	0.35
PhyloP100		-2.4
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: rs10488040; hg19: chr7-77365365;