Variant 1-37806988-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_024640.4(YRDC):c.505-12C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 1,613,964 control chromosomes in the GnomAD database, including 65,371 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.23 ( 4840 hom., cov: 33)

Exomes 𝑓: 0.28 ( 60531 hom. )

Consequence

YRDC
NM_024640.4 splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.00003630

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0360

Variant links:

Genes affected

C1orf122 (HGNC:24789): (chromosome 1 open reading frame 122)

C1orf122 links:

YRDC (HGNC:28905): (yrdC N6-threonylcarbamoyltransferase domain containing) Predicted to enable nucleotidyltransferase activity and tRNA binding activity. Acts upstream of or within negative regulation of transport. Predicted to be located in membrane and mitochondrion. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

YRDC links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 1-37806988-G-A is Benign according to our data. Variant chr1-37806988-G-A is described in ClinVar as [Benign]. Clinvar id is 1970918.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
YRDC	NM_024640.4 linkuse as main transcript	c.505-12C>T		splice_polypyrimidine_tract_variant, intron_variant		ENST00000373044.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1orf122	ENST00000373043.1 linkuse as main transcript	c.-1697G>A		5_prime_UTR_variant	1/2	1			Q6ZSJ8-2
YRDC	ENST00000373044.3 linkuse as main transcript	c.505-12C>T		splice_polypyrimidine_tract_variant, intron_variant		1	NM_024640.4	P1

Frequencies

GnomAD3 genomes

AF:

0.233

AC:

35372

AN:

152102

Hom.:

4839

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0827

Gnomad AMI

AF:

0.0791

Gnomad AMR

AF:

0.211

Gnomad ASJ

AF:

0.310

Gnomad EAS

AF:

0.275

Gnomad SAS

AF:

0.262

Gnomad FIN

AF:

0.394

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.296

Gnomad OTH

AF:

0.230

GnomAD3 exomes

AF:

0.267

AC:

66983

AN:

251278

Hom.:

9639

AF XY:

0.269

AC XY:

36519

AN XY:

135834

show subpopulations

Gnomad AFR exome

AF:

0.0805

Gnomad AMR exome

AF:

0.207

Gnomad ASJ exome

AF:

0.313

Gnomad EAS exome

AF:

0.273

Gnomad SAS exome

AF:

0.253

Gnomad FIN exome

AF:

0.381

Gnomad NFE exome

AF:

0.288

Gnomad OTH exome

AF:

0.271

GnomAD4 exome

AF:

0.284

AC:

414856

AN:

1461744

Hom.:

60531

Cov.:

AF XY:

0.284

AC XY:

206281

AN XY:

727190

show subpopulations

Gnomad4 AFR exome

AF:

0.0736

Gnomad4 AMR exome

AF:

0.208

Gnomad4 ASJ exome

AF:

0.317

Gnomad4 EAS exome

AF:

0.319

Gnomad4 SAS exome

AF:

0.253

Gnomad4 FIN exome

AF:

0.379

Gnomad4 NFE exome

AF:

0.291

Gnomad4 OTH exome

AF:

0.260

GnomAD4 genome

AF:

0.232

AC:

35367

AN:

152220

Hom.:

4840

Cov.:

AF XY:

0.238

AC XY:

17707

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.0825

Gnomad4 AMR

AF:

0.211

Gnomad4 ASJ

AF:

0.310

Gnomad4 EAS

AF:

0.275

Gnomad4 SAS

AF:

0.261

Gnomad4 FIN

AF:

0.394

Gnomad4 NFE

AF:

0.296

Gnomad4 OTH

AF:

0.229

Alfa

AF:

0.270

Hom.:

3800

Bravo

AF:

0.209

Asia WGS

AF:

0.293

AC:

1019

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 30, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

3.8

DANN

Benign

0.66

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000036

dbscSNV1_RF

Benign

0.0

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over