rs2253977

Variant names:

• chr20-3958493-T-A
• rs2253977
• NM_001134337.3:c.143+5382A>T

Your query was ambiguous. Multiple possible variants found:

• chr20-3958493-T-A
• chr20-3958493-T-C
• chr20-3958493-T-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001134337.3(RNF24):​c.143+5382A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: RNF24 NM_001134337.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240

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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNF24	NM_001134337.3	c.143+5382A>T		intron_variant	Intron 2 of 5	ENST00000358395.11	NP_001127809.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF24	ENST00000358395.11	c.143+5382A>T		intron_variant	Intron 2 of 5	1	NM_001134337.3	ENSP00000351166.6
RNF24	ENST00000545616.2	c.206+5382A>T		intron_variant	Intron 3 of 6	1		ENSP00000444711.1
RNF24	ENST00000336095.10	c.143+5382A>T		intron_variant	Intron 2 of 5	1		ENSP00000336753.5
RNF24	ENST00000432261.6	c.206+5382A>T		intron_variant	Intron 2 of 5	5		ENSP00000388550.2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.62

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: rs2253977; hg19: chr20-3939140;