rs1730874

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001031732.4(YTHDC1):​c.1825-535C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.994 in 152,332 control chromosomes in the GnomAD database, including 75,291 homozygotes. 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 0.99 ( 75291 hom., cov: 32)

Consequence

YTHDC1
NM_001031732.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.383
Variant links:
Genes affected
YTHDC1 (HGNC:30626): (YTH N6-methyladenosine RNA binding protein C1) Enables N6-methyladenosine-containing RNA binding activity. Involved in mRNA export from nucleus; mRNA splice site selection; and regulation of gene expression. Located in nuclear speck and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
YTHDC1NM_001031732.4 linkc.1825-535C>T intron_variant Intron 15 of 16 ENST00000344157.9 NP_001026902.1 Q96MU7-1
YTHDC1NM_001330698.2 linkc.1849-535C>T intron_variant Intron 15 of 16 NP_001317627.1 Q96MU7J3QR07
YTHDC1NM_133370.4 linkc.1771-535C>T intron_variant Intron 14 of 15 NP_588611.2 Q96MU7-2
YTHDC1XM_005265708.4 linkc.1795-535C>T intron_variant Intron 14 of 15 XP_005265765.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
YTHDC1ENST00000344157.9 linkc.1825-535C>T intron_variant Intron 15 of 16 1 NM_001031732.4 ENSP00000339245.4 Q96MU7-1
YTHDC1ENST00000355665.7 linkc.1771-535C>T intron_variant Intron 14 of 15 1 ENSP00000347888.3 Q96MU7-2
YTHDC1ENST00000579690.5 linkc.1849-535C>T intron_variant Intron 15 of 16 5 ENSP00000463982.1 J3QR07
YTHDC1ENST00000507529.1 linkc.94-535C>T intron_variant Intron 2 of 2 3 ENSP00000461990.1 J3KRG5

Frequencies

GnomAD3 genomes
AF:
0.994
AC:
151331
AN:
152214
Hom.:
75233
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.981
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
0.996
Gnomad ASJ
AF:
0.998
Gnomad EAS
AF:
1.00
Gnomad SAS
AF:
1.00
Gnomad FIN
AF:
1.00
Gnomad MID
AF:
0.991
Gnomad NFE
AF:
1.00
Gnomad OTH
AF:
0.994
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.994
AC:
151448
AN:
152332
Hom.:
75291
Cov.:
32
AF XY:
0.995
AC XY:
74085
AN XY:
74492
show subpopulations
Gnomad4 AFR
AF:
0.981
Gnomad4 AMR
AF:
0.996
Gnomad4 ASJ
AF:
0.998
Gnomad4 EAS
AF:
1.00
Gnomad4 SAS
AF:
1.00
Gnomad4 FIN
AF:
1.00
Gnomad4 NFE
AF:
1.00
Gnomad4 OTH
AF:
0.994
Alfa
AF:
0.996
Hom.:
9367
Bravo
AF:
0.994
Asia WGS
AF:
0.999
AC:
3475
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
0.71
DANN
Benign
0.15

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

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

Other links and lift over

dbSNP: rs1730874; hg19: chr4-69182701; API