rs420013

Variant names:

• chr2-7021455-C-A
• rs420013
• NM_014746.6:c.509+775C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-7021455-C-A
• chr2-7021455-C-G
• chr2-7021455-C-T

Variant summary

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

The NM_014746.6(RNF144A):​c.509+775C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,732 control chromosomes in the GnomAD database, including 16,390 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 0.45 (16390 hom., cov: 31)
• Consequence: RNF144A NM_014746.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 0 publications found

Genes affected

RNF144A (HGNC:20457): (ring finger protein 144A) This gene encodes a member of a family of RING finger domain-containing E3 ubiquitin ligases that also includes parkin and parc. The expression of this gene is induced by DNA damage. The encoded protein interacts with the cytoplasmic DNA-dependent protein kinase, catalytic subunit (DNA-PKcs) and promotes its degradation through ubiquitination. The orthologous mouse protein has been shown to interact with a ubiquitin-conjugating enzyme involved in embryonic development. [provided by RefSeq, Mar 2017]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNF144A	NM_014746.6	c.509+775C>A		intron_variant	Intron 6 of 8	ENST00000320892.11	NP_055561.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF144A	ENST00000320892.11	c.509+775C>A		intron_variant	Intron 6 of 8	1	NM_014746.6	ENSP00000321330.6
RNF144A	ENST00000432850.1	c.494+775C>A		intron_variant	Intron 4 of 6	3		ENSP00000411616.1
RNF144A	ENST00000467276.5	n.630+687C>A		intron_variant	Intron 3 of 5	3
RNF144A	ENST00000480970.1	n.555+775C>A		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68196 AN: 151614 Hom.: 16361 Cov.: 31

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.450 AC: 68269 AN: 151732 Hom.: 16390 Cov.: 31 AF XY: 0.458 AC XY: 33957 AN XY: 74154

African (AFR) AF: 0.306 AC: 12639 AN: 41352

American (AMR) AF: 0.513 AC: 7830 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1610 AN: 3470

East Asian (EAS) AF: 0.716 AC: 3679 AN: 5140

South Asian (SAS) AF: 0.748 AC: 3595 AN: 4808

European-Finnish (FIN) AF: 0.490 AC: 5153 AN: 10516

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32350 AN: 67880

Other (OTH) AF: 0.444 AC: 932 AN: 2098

Alfa AF: 0.469 Hom.: 8543

Bravo AF: 0.443

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.082
DANN	Benign	0.87
PhyloP100		-1.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs420013; hg19: chr2-7161586;