rs6956726

chr7-77745529-C-T

Variant summary

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

The NM_198467.3(RSBN1L):c.704-3895C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 152,016 control chromosomes in the GnomAD database, including 27,908 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 0.58 (27908 hom., cov: 31)
• Consequence: RSBN1L NM_198467.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.294

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RSBN1L	NM_198467.3	c.704-3895C>T		intron_variant		ENST00000334955.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RSBN1L	ENST00000334955.13	c.704-3895C>T		intron_variant		1	NM_198467.3	P1
RSBN1L	ENST00000445288.5	c.-107-3895C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88403 AN: 151898 Hom.: 27842 Cov.: 31

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.582 AC: 88534 AN: 152016 Hom.: 27908 Cov.: 31 AF XY: 0.575 AC XY: 42714 AN XY: 74248

Gnomad4 AFR AF: 0.838

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.578

Alfa AF: 0.530 Hom.: 3846

Bravo AF: 0.597

Asia WGS AF: 0.544 AC: 1893 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	0.24

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: rs6956726; hg19: chr7-77374846;