rs241605

chr20-3934417-C-T

Variant summary

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

The NM_001134337.3(RNF24):c.309-216G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 152,066 control chromosomes in the GnomAD database, including 8,298 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 0.32 (8298 hom., cov: 31)
• Consequence: RNF24 NM_001134337.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116

Genes affected

RNF24 (HGNC:13779): (ring finger protein 24) This gene encodes an integral membrane protein that contains a RING-type zinc finger. The encoded protein may interact with multiple transient receptor potential cation channel subfamily C (TRPC) proteins and regulate the trafficking and insertion of these proteins into the plasma membrane. [provided by RefSeq, Mar 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RNF24	NM_001134337.3	c.309-216G>A		intron_variant		ENST00000358395.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNF24	ENST00000358395.11	c.309-216G>A		intron_variant		1	NM_001134337.3	P1
RNF24	ENST00000336095.10	c.309-216G>A		intron_variant		1		P1
RNF24	ENST00000545616.2	c.372-216G>A		intron_variant		1
RNF24	ENST00000432261.6	c.372-216G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48167 AN: 151946 Hom.: 8288 Cov.: 31

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.317 AC: 48210 AN: 152066 Hom.: 8298 Cov.: 31 AF XY: 0.313 AC XY: 23269 AN XY: 74338

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.299

Alfa AF: 0.278 Hom.: 9801

Bravo AF: 0.318

Asia WGS AF: 0.328 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	8.6
Dann	Benign	0.63

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: rs241605; hg19: chr20-3915064;