NM_016271.5:c.110+2143G>A

Variant names:

• chr18-32095029-G-A
• rs4799327
• NM_016271.5:c.110+2143G>A

Variant summary

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

The NM_016271.5(RNF138):​c.110+2143G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,120 control chromosomes in the GnomAD database, including 2,219 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 0.17 (2219 hom., cov: 33)
• Consequence: RNF138 NM_016271.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 9 publications found

Genes affected

RNF138 (HGNC:17765): (ring finger protein 138) The protein encoded by this gene contains a RING finger, a motif present in a variety of functionally distinct proteins and known to be involved in protein-DNA and protein-protein interactions. Alternatively spliced transcript variants encoding distinct isoforms have been observed. [provided by RefSeq, Jul 2008]

ENSG00000263917 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNF138	NM_016271.5	c.110+2143G>A		intron_variant	Intron 2 of 7	ENST00000261593.8	NP_057355.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF138	ENST00000261593.8	c.110+2143G>A		intron_variant	Intron 2 of 7	1	NM_016271.5	ENSP00000261593.3

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25402 AN: 152002 Hom.: 2211 Cov.: 33

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.0955

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.167 AC: 25447 AN: 152120 Hom.: 2219 Cov.: 33 AF XY: 0.170 AC XY: 12654 AN XY: 74380

African (AFR) AF: 0.195 AC: 8077 AN: 41478

American (AMR) AF: 0.158 AC: 2418 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 813 AN: 3466

East Asian (EAS) AF: 0.0959 AC: 497 AN: 5180

South Asian (SAS) AF: 0.201 AC: 968 AN: 4826

European-Finnish (FIN) AF: 0.169 AC: 1790 AN: 10566

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10344 AN: 67996

Other (OTH) AF: 0.175 AC: 369 AN: 2114

Alfa AF: 0.157 Hom.: 8498

Bravo AF: 0.164

Asia WGS AF: 0.169 AC: 590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.3
DANN	Benign	0.57
PhyloP100		0.0070
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: rs4799327; hg19: chr18-29674992;