rs2306921

Variant names:

• chr7-4799634-G-A
• rs2306921
• NM_018059.5:c.3118C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-4799634-G-A
• chr7-4799634-G-C
• chr7-4799634-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_018059.5(RADIL):​c.3118C>T​(p.Leu1040Leu) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000344 in 1,452,834 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 34)
  • Exomes 𝑓: 0.0000034 (0 hom.)
• Consequence: RADIL NM_018059.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.85
• Publications: 7 publications found

Genes affected

RADIL (HGNC:22226): (Rap associating with DIL domain) Predicted to enable GTPase binding activity. Acts upstream of or within substrate adhesion-dependent cell spreading. Located in microtubule. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.59).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018059.5. 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
	RADIL	NM_018059.5	MANE Select	c.3118C>T	p.Leu1040Leu	synonymous	Exon 14 of 15	NP_060529.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RADIL	ENST00000399583.4	TSL:5 MANE Select	c.3118C>T	p.Leu1040Leu	synonymous	Exon 14 of 15	ENSP00000382492.3
	RADIL	ENST00000472999.5	TSL:1	n.1142C>T		non_coding_transcript_exon	Exon 4 of 5
	RADIL	ENST00000445392.5	TSL:5	n.*1889C>T		non_coding_transcript_exon	Exon 14 of 15	ENSP00000413403.1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome AF: 0.00000344 AC: 5 AN: 1452834 Hom.: 0 Cov.: 33 AF XY: 0.00000277 AC XY: 2 AN XY: 722060

African (AFR) AF: 0.0000599 AC: 2 AN: 33376

American (AMR) AF: 0.00 AC: 0 AN: 43544

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25686

East Asian (EAS) AF: 0.0000760 AC: 3 AN: 39452

South Asian (SAS) AF: 0.00 AC: 0 AN: 85226

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 51500

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5744

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1108296

Other (OTH) AF: 0.00 AC: 0 AN: 60010

GnomAD4 genome Cov.: 34

Alfa AF: 0.000245 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	4.9
DANN	Benign	0.84
PhyloP100		3.9

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: rs2306921; hg19: chr7-4839265;