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. The variant received -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
• Publications: 10 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: Likely_benign. The variant received -2 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001134337.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNF24	NM_001134337.3	MANE Select	c.143+5382A>T		intron	N/A	NP_001127809.1
	RNF24	NM_001134338.3		c.206+5382A>T		intron	N/A	NP_001127810.1
	RNF24	NM_001321749.2		c.143+5382A>T		intron	N/A	NP_001308678.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNF24	ENST00000358395.11	TSL:1 MANE Select	c.143+5382A>T		intron	N/A	ENSP00000351166.6
	RNF24	ENST00000545616.2	TSL:1	c.206+5382A>T		intron	N/A	ENSP00000444711.1
	RNF24	ENST00000336095.10	TSL:1	c.143+5382A>T		intron	N/A	ENSP00000336753.5

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.62
PhyloP100		-0.24

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: rs2253977; hg19: chr20-3939140;