6-37366020-C-T

Variant summary

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

The NM_003958.4(RNF8):c.241-2464C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 151,938 control chromosomes in the GnomAD database, including 27,055 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 (27055 hom., cov: 30)
• Consequence: RNF8 NM_003958.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57

Genes affected

RNF8 (HGNC:10071): (ring finger protein 8) The protein encoded by this gene contains a RING finger motif and an FHA domain. This protein has been shown to interact with several class II ubiquitin-conjugating enzymes (E2), including UBE2E1/UBCH6, UBE2E2, and UBE2E3, and may act as an ubiquitin ligase (E3) in the ubiquitination of certain nuclear proteins. This protein is also known to play a role in the DNA damage response and depletion of this protein causes cell growth inhibition and cell cycle arrest. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RNF8	NM_003958.4	c.241-2464C>T		intron_variant		ENST00000373479.9
RNF8	NM_183078.3	c.241-2464C>T		intron_variant
RNF8	NR_046399.2	n.423-2358C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNF8	ENST00000373479.9	c.241-2464C>T		intron_variant		1	NM_003958.4	P1

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87524 AN: 151820 Hom.: 27015 Cov.: 30

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.577 AC: 87625 AN: 151938 Hom.: 27055 Cov.: 30 AF XY: 0.578 AC XY: 42901 AN XY: 74228

Gnomad4 AFR AF: 0.782

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.481

Gnomad4 EAS AF: 0.769

Gnomad4 SAS AF: 0.654

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.574

Alfa AF: 0.484 Hom.: 8327

Bravo AF: 0.598

Asia WGS AF: 0.710 AC: 2472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	9.4
Dann	Benign	0.42

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: rs195385; hg19: chr6-37333796;