rs651627

chr12-120571395-C-T

Variant summary

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

The NM_014868.5(RNF10):c.2142+104C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 836,396 control chromosomes in the GnomAD database, including 41,292 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 0.26 (5975 hom., cov: 31)
  • Exomes 𝑓: 0.31 (35317 hom.)
• Consequence: RNF10 NM_014868.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.727

Genes affected

RNF10 (HGNC:10055): (ring finger protein 10) The protein encoded by this gene contains a ring finger motif, which is known to be involved in protein-protein interactions. The specific function of this protein has not yet been determined. EST data suggests the existence of multiple alternatively spliced transcript variants, however, their full length nature is not known. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RNF10	NM_014868.5	c.2142+104C>T		intron_variant		ENST00000325954.9
RNF10	NM_001330474.2	c.2157+104C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNF10	ENST00000325954.9	c.2142+104C>T		intron_variant		1	NM_014868.5	P1

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39595 AN: 151924 Hom.: 5962 Cov.: 31

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.251

GnomAD4 exome AF: 0.315 AC: 215426 AN: 684354 Hom.: 35317 AF XY: 0.315 AC XY: 113489 AN XY: 359872

Gnomad4 AFR exome AF: 0.111

Gnomad4 AMR exome AF: 0.308

Gnomad4 ASJ exome AF: 0.236

Gnomad4 EAS exome AF: 0.509

Gnomad4 SAS exome AF: 0.304

Gnomad4 FIN exome AF: 0.327

Gnomad4 NFE exome AF: 0.314

Gnomad4 OTH exome AF: 0.298

GnomAD4 genome AF: 0.261 AC: 39620 AN: 152042 Hom.: 5975 Cov.: 31 AF XY: 0.264 AC XY: 19646 AN XY: 74298

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.247

Alfa AF: 0.288 Hom.: 1658

Bravo AF: 0.251

Asia WGS AF: 0.354 AC: 1233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	2.2
Dann	Benign	0.80

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: rs651627; hg19: chr12-121009198; COSMIC: COSV58045399; COSMIC: COSV58045399;