rs6956726

Variant names:

• chr7-77745529-C-T
• rs6956726
• NM_198467.3:c.704-3895C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.91).
• 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 rank	MANE	Protein	UniProt
RSBN1L	NM_198467.3	c.704-3895C>T		intron_variant	Intron 2 of 7	ENST00000334955.13	NP_940869.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RSBN1L	ENST00000334955.13	c.704-3895C>T		intron_variant	Intron 2 of 7	1	NM_198467.3	ENSP00000334040.7
RSBN1L	ENST00000445288.5	c.-107-3895C>T		intron_variant	Intron 2 of 7	5		ENSP00000393888.1

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

African (AFR) AF: 0.838 AC: 34784 AN: 41516

American (AMR) AF: 0.507 AC: 7755 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2045 AN: 3470

East Asian (EAS) AF: 0.314 AC: 1626 AN: 5172

South Asian (SAS) AF: 0.558 AC: 2690 AN: 4818

European-Finnish (FIN) AF: 0.401 AC: 4222 AN: 10518

Middle Eastern (MID) AF: 0.586 AC: 171 AN: 292

European-Non Finnish (NFE) AF: 0.492 AC: 33405 AN: 67932

Other (OTH) AF: 0.578 AC: 1220 AN: 2110

Alfa AF: 0.539 Hom.: 4108

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
PhyloP100		-0.29
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: rs6956726; hg19: chr7-77374846;