4-68316983-G-T

Variant names:

• chr4-68316983-G-T
• rs1730874
• NM_001031732.4:c.1825-535C>A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001031732.4(YTHDC1):​c.1825-535C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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.

• Frequency: Genomes: not found (cov: 32)
• Consequence: YTHDC1 NM_001031732.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383

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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
YTHDC1	NM_001031732.4	c.1825-535C>A		intron_variant	Intron 15 of 16	ENST00000344157.9	NP_001026902.1
YTHDC1	NM_001330698.2	c.1849-535C>A		intron_variant	Intron 15 of 16		NP_001317627.1
YTHDC1	NM_133370.4	c.1771-535C>A		intron_variant	Intron 14 of 15		NP_588611.2
YTHDC1	XM_005265708.4	c.1795-535C>A		intron_variant	Intron 14 of 15		XP_005265765.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
YTHDC1	ENST00000344157.9	c.1825-535C>A		intron_variant	Intron 15 of 16	1	NM_001031732.4	ENSP00000339245.4
YTHDC1	ENST00000355665.7	c.1771-535C>A		intron_variant	Intron 14 of 15	1		ENSP00000347888.3
YTHDC1	ENST00000579690.5	c.1849-535C>A		intron_variant	Intron 15 of 16	5		ENSP00000463982.1
YTHDC1	ENST00000507529.1	c.94-535C>A		intron_variant	Intron 2 of 2	3		ENSP00000461990.1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.57
DANN	Benign	0.18

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: rs1730874; hg19: chr4-69182701;