X-53430674-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001031745.5(RIBC1):​c.942C>T​(p.Thr314Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 1,201,851 control chromosomes in the GnomAD database, including 82,331 homozygotes. There are 172,046 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: 𝑓 0.52 (12037 hom., 16884 hem., cov: 23)
  • Exomes 𝑓: 0.43 (70294 hom. 155162 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: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP7: Synonymous conserved (PhyloP=-0.172 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.524 AC: 57987 AN: 110582 Hom.: 12042 Cov.: 23

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.435

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.505

GnomAD4 exome AF: 0.432 AC: 471778 AN: 1091216 Hom.: 70294 Cov.: 35 AF XY: 0.433 AC XY: 155162 AN XY: 358002

African (AFR) AF: 0.803 AC: 21136 AN: 26327

American (AMR) AF: 0.478 AC: 16303 AN: 34113

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 9630 AN: 19265

East Asian (EAS) AF: 0.498 AC: 14968 AN: 30057

South Asian (SAS) AF: 0.507 AC: 26929 AN: 53105

European-Finnish (FIN) AF: 0.395 AC: 15847 AN: 40089

Middle Eastern (MID) AF: 0.388 AC: 1599 AN: 4125

European-Non Finnish (NFE) AF: 0.411 AC: 344586 AN: 838247

Other (OTH) AF: 0.453 AC: 20780 AN: 45888

GnomAD4 genome AF: 0.524 AC: 58026 AN: 110635 Hom.: 12037 Cov.: 23 AF XY: 0.513 AC XY: 16884 AN XY: 32901

African (AFR) AF: 0.792 AC: 24084 AN: 30421

American (AMR) AF: 0.475 AC: 4943 AN: 10397

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1304 AN: 2639

East Asian (EAS) AF: 0.471 AC: 1649 AN: 3500

South Asian (SAS) AF: 0.521 AC: 1361 AN: 2613

European-Finnish (FIN) AF: 0.374 AC: 2191 AN: 5862

Middle Eastern (MID) AF: 0.421 AC: 91 AN: 216

European-Non Finnish (NFE) AF: 0.404 AC: 21328 AN: 52804

Other (OTH) AF: 0.506 AC: 764 AN: 1509

Alfa AF: 0.451 Hom.: 52921

Bravo AF: 0.544

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.66
PhyloP100		-0.17

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1264013; hg19: chrX-53457622;