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. Variant got -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

Genes affected

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

ACMG classification

Verdict is Likely_benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RIBC1	NM_001031745.5	c.942C>A	p.Thr314Thr	synonymous_variant	Exon 7 of 8	ENST00000375327.6	NP_001026915.1
RIBC1	NM_001267053.4	c.597C>A	p.Thr199Thr	synonymous_variant	Exon 6 of 6		NP_001253982.1
RIBC1	XM_005261988.5	c.942C>A	p.Thr314Thr	synonymous_variant	Exon 7 of 8		XP_005262045.1
RIBC1	XM_005261990.5	c.597C>A	p.Thr199Thr	synonymous_variant	Exon 6 of 7		XP_005262047.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RIBC1	ENST00000375327.6	c.942C>A	p.Thr314Thr	synonymous_variant	Exon 7 of 8	1	NM_001031745.5	ENSP00000364476.3
RIBC1	ENST00000414955.6	c.597C>A	p.Thr199Thr	synonymous_variant	Exon 6 of 6	2		ENSP00000401463.2

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

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000188

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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: rs1264013; hg19: chrX-53457622;