chr12-120536707-C-T

Position:

• chr12-120536707-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.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

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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RNF10	NM_014868.5	c.157+1739C>T		intron_variant		ENST00000325954.9
RNF10	NM_001330474.2	c.157+1739C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNF10	ENST00000325954.9	c.157+1739C>T		intron_variant		1	NM_014868.5	P1

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

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.187

Alfa AF: 0.175 Hom.: 424

Bravo AF: 0.185

Asia WGS AF: 0.173 AC: 602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.8
DANN	Benign	0.67

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: rs614226; hg19: chr12-120974510;