rs614226

Variant names:

• chr12-120536707-C-T
• rs614226
• NM_014868.5:c.157+1739C>T

Variant summary

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

The NM_014868.5(RNF10):​c.157+1739C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,102 control chromosomes in the GnomAD database, including 2,665 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 0.18 (2665 hom., cov: 32)
• Consequence: RNF10 NM_014868.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178
• Publications: 23 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014868.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNF10	NM_014868.5	MANE Select	c.157+1739C>T		intron	N/A	NP_055683.3
	RNF10	NM_001330474.2		c.157+1739C>T		intron	N/A	NP_001317403.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNF10	ENST00000325954.9	TSL:1 MANE Select	c.157+1739C>T		intron	N/A	ENSP00000322242.4
	RNF10	ENST00000413266.6	TSL:5	c.157+1739C>T		intron	N/A	ENSP00000415682.2
	RNF10	ENST00000537997.1	TSL:4	c.-95+1165C>T		intron	N/A	ENSP00000443235.1

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27489 AN: 151982 Hom.: 2668 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.181 AC: 27498 AN: 152102 Hom.: 2665 Cov.: 32 AF XY: 0.179 AC XY: 13321 AN XY: 74352

African (AFR) AF: 0.211 AC: 8745 AN: 41490

American (AMR) AF: 0.139 AC: 2124 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1278 AN: 3472

East Asian (EAS) AF: 0.156 AC: 809 AN: 5172

South Asian (SAS) AF: 0.185 AC: 893 AN: 4826

European-Finnish (FIN) AF: 0.132 AC: 1392 AN: 10578

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11540 AN: 67988

Other (OTH) AF: 0.187 AC: 395 AN: 2110

Alfa AF: 0.174 Hom.: 3927

Bravo AF: 0.185

Asia WGS AF: 0.173 AC: 602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.8
DANN	Benign	0.67
PhyloP100		0.18
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: rs614226; hg19: chr12-120974510;