chr20-3934417-C-T

Variant names:

• chr20-3934417-C-T
• rs241605
• NM_001134337.3:c.309-216G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
RNF24	NM_001134337.3	c.309-216G>A		intron_variant	Intron 5 of 5	ENST00000358395.11	NP_001127809.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF24	ENST00000358395.11	c.309-216G>A		intron_variant	Intron 5 of 5	1	NM_001134337.3	ENSP00000351166.6
RNF24	ENST00000545616.2	c.372-216G>A		intron_variant	Intron 6 of 6	1		ENSP00000444711.1
RNF24	ENST00000336095.10	c.309-216G>A		intron_variant	Intron 5 of 5	1		ENSP00000336753.5
RNF24	ENST00000432261.6	c.372-216G>A		intron_variant	Intron 5 of 5	5		ENSP00000388550.2

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

African (AFR) AF: 0.458 AC: 18987 AN: 41478

American (AMR) AF: 0.217 AC: 3317 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1277 AN: 3466

East Asian (EAS) AF: 0.285 AC: 1472 AN: 5160

South Asian (SAS) AF: 0.364 AC: 1753 AN: 4820

European-Finnish (FIN) AF: 0.227 AC: 2405 AN: 10572

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.267 AC: 18120 AN: 67964

Other (OTH) AF: 0.299 AC: 630 AN: 2110

Alfa AF: 0.284 Hom.: 24289

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
PhyloP100		0.12
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: rs241605; hg19: chr20-3915064;