4-68314262-C-G

Variant names:

• chr4-68314262-C-G
• rs751003108
• NM_001031732.4:c.2021G>C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001031732.4(YTHDC1):​c.2021G>C​(p.Arg674Pro) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R674Q) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: YTHDC1 NM_001031732.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.10

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.2760054).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
YTHDC1	NM_001031732.4	c.2021G>C	p.Arg674Pro	missense_variant	Exon 17 of 17	ENST00000344157.9	NP_001026902.1
YTHDC1	NM_001330698.2	c.2045G>C	p.Arg682Pro	missense_variant	Exon 17 of 17		NP_001317627.1
YTHDC1	NM_133370.4	c.1967G>C	p.Arg656Pro	missense_variant	Exon 16 of 16		NP_588611.2
YTHDC1	XM_005265708.4	c.1991G>C	p.Arg664Pro	missense_variant	Exon 16 of 16		XP_005265765.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
YTHDC1	ENST00000344157.9	c.2021G>C	p.Arg674Pro	missense_variant	Exon 17 of 17	1	NM_001031732.4	ENSP00000339245.4
YTHDC1	ENST00000355665.7	c.1967G>C	p.Arg656Pro	missense_variant	Exon 16 of 16	1		ENSP00000347888.3
YTHDC1	ENST00000579690.5	c.2045G>C	p.Arg682Pro	missense_variant	Exon 17 of 17	5		ENSP00000463982.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.89
BayesDel_addAF	Uncertain	0.037	T
BayesDel_noAF	Benign	-0.18
CADD	Pathogenic	27
DANN	Uncertain	0.99
DEOGEN2	Benign	0.026	T;.;.
Eigen	Uncertain	0.40
Eigen_PC	Uncertain	0.46
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.90	D;D;D
M_CAP	Benign	0.039	D
MetaRNN	Benign	0.28	T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.8	L;.;.
PrimateAI	Pathogenic	0.89	D
PROVEAN	Benign	-1.4	N;N;.
REVEL	Benign	0.18
Sift	Uncertain	0.0070	D;D;.
Sift4G	Benign	0.13	T;T;T
Polyphen		0.98	D;D;.
Vest4		0.57
MutPred		0.23		Loss of methylation at R674 (P = 0.015);.;.;
MVP		0.043
MPC		0.86
ClinPred		0.85	D
GERP RS		4.7
Varity_R		0.59
gMVP		0.25

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: rs751003108; hg19: chr4-69179980;