Genetic Variant RIBC1:p.Thr314Thr (chrX-53430674-C-A) – ACMG Classification: Likely_benign (-3 pts)

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.172

Publications

19 publications found

Variant links:

Genes affected

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

RIBC1 links:

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ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RIBC1	NM_001031745.5 link	c.942C>A	p.Thr314Thr	synonymous_variant	Exon 7 of 8	ENST00000375327.6	NP_001026915.1	Q8N443-1A0A024R9X7
RIBC1	NM_001267053.4 link	c.597C>A	p.Thr199Thr	synonymous_variant	Exon 6 of 6		NP_001253982.1	Q8N443-3
RIBC1	XM_005261988.5 link	c.942C>A	p.Thr314Thr	synonymous_variant	Exon 7 of 8		XP_005262045.1	Q8N443-1A0A024R9X7
RIBC1	XM_005261990.5 link	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 link	c.942C>A	p.Thr314Thr	synonymous_variant	Exon 7 of 8	1	NM_001031745.5	ENSP00000364476.3		Q8N443-1
RIBC1	ENST00000414955.6 link	c.597C>A	p.Thr199Thr	synonymous_variant	Exon 6 of 6	2		ENSP00000401463.2		Q8N443-3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

9.16e-7

AC:

AN:

1091464

Hom.:

Cov.:

AF XY:

0.00000279

AC XY:

AN XY:

358166

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

26329

American (AMR)

AF:

0.00

AC:

AN:

34151

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

19266

East Asian (EAS)

AF:

0.00

AC:

AN:

30073

South Asian (SAS)

AF:

0.0000188

AC:

AN:

53116

European-Finnish (FIN)

AF:

0.00

AC:

AN:

40110

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4125

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

838399

Other (OTH)

AF:

0.00

AC:

AN:

45895

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

52921

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

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over