rs1264013

Variant names:

• chrX-53430674-C-A
• rs1264013
• NM_001031745.5:c.942C>A

Your query was ambiguous. Multiple possible variants found:

• chrX-53430674-C-A
• chrX-53430674-C-T

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001031745.5(RIBC1):​c.942C>A​(p.Thr314Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000916 in 1,091,464 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. 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: 23)
  • Exomes 𝑓: 9.2e-7 (0 hom. 1 hem.)
• Consequence: RIBC1 NM_001031745.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172
• Publications: 19 publications found

Genes affected

RIBC1 (HGNC:26537): (RIB43A domain with coiled-coils 1)

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP7: Synonymous conserved (PhyloP=-0.172 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001031745.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RIBC1	NM_001031745.5	MANE Select	c.942C>A	p.Thr314Thr	synonymous	Exon 7 of 8	NP_001026915.1	Q8N443-1
	RIBC1	NM_001267053.4		c.597C>A	p.Thr199Thr	synonymous	Exon 6 of 6	NP_001253982.1	Q8N443-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RIBC1	ENST00000375327.6	TSL:1 MANE Select	c.942C>A	p.Thr314Thr	synonymous	Exon 7 of 8	ENSP00000364476.3	Q8N443-1
	RIBC1	ENST00000868183.1		c.942C>A	p.Thr314Thr	synonymous	Exon 7 of 8	ENSP00000538242.1
	RIBC1	ENST00000929472.1		c.942C>A	p.Thr314Thr	synonymous	Exon 8 of 9	ENSP00000599531.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome AF: 9.16e-7 AC: 1 AN: 1091464 Hom.: 0 Cov.: 35 AF XY: 0.00000279 AC XY: 1 AN XY: 358166

African (AFR) AF: 0.00 AC: 0 AN: 26329

American (AMR) AF: 0.00 AC: 0 AN: 34151

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19266

East Asian (EAS) AF: 0.00 AC: 0 AN: 30073

South Asian (SAS) AF: 0.0000188 AC: 1 AN: 53116

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40110

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4125

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 838399

Other (OTH) AF: 0.00 AC: 0 AN: 45895

GnomAD4 genome Cov.: 23

Alfa AF: 0.00 Hom.: 52921

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.57
PhyloP100		-0.17

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: rs1264013; hg19: chrX-53457622;