rs566379464

Variant names:

• chr4-68337208-TTCCTCCTCC-T
• rs566379464
• NM_001031732.4:c.693_701delGGAGGAGGA

Your query was ambiguous. Multiple possible variants found:

• chr4-68337208-TTCCTCCTCC-T
• chr4-68337208-TTCCTCCTCC-TTCC
• chr4-68337208-TTCCTCCTCC-TTCCTCC
• chr4-68337208-TTCCTCCTCC-TTCCTCCTCCTCC

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001031732.4(YTHDC1):​c.693_701delGGAGGAGGA​(p.Glu232_Glu234del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00000139 in 1,437,604 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: YTHDC1 NM_001031732.4 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.50

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 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
YTHDC1	NM_001031732.4	c.693_701delGGAGGAGGA	p.Glu232_Glu234del	disruptive_inframe_deletion	Exon 4 of 17	ENST00000344157.9	NP_001026902.1
YTHDC1	NM_001330698.2	c.693_701delGGAGGAGGA	p.Glu232_Glu234del	disruptive_inframe_deletion	Exon 4 of 17		NP_001317627.1
YTHDC1	NM_133370.4	c.693_701delGGAGGAGGA	p.Glu232_Glu234del	disruptive_inframe_deletion	Exon 4 of 16		NP_588611.2
YTHDC1	XM_005265708.4	c.693_701delGGAGGAGGA	p.Glu232_Glu234del	disruptive_inframe_deletion	Exon 4 of 16		XP_005265765.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
YTHDC1	ENST00000344157.9	c.693_701delGGAGGAGGA	p.Glu232_Glu234del	disruptive_inframe_deletion	Exon 4 of 17	1	NM_001031732.4	ENSP00000339245.4
YTHDC1	ENST00000355665.7	c.693_701delGGAGGAGGA	p.Glu232_Glu234del	disruptive_inframe_deletion	Exon 4 of 16	1		ENSP00000347888.3
YTHDC1	ENST00000579690.5	c.693_701delGGAGGAGGA	p.Glu232_Glu234del	disruptive_inframe_deletion	Exon 4 of 17	5		ENSP00000463982.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000408 AC: 1 AN: 244920 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 132262

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000333

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000139 AC: 2 AN: 1437604 Hom.: 0 AF XY: 0.00000140 AC XY: 1 AN XY: 716224

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000234

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs566379464; hg19: chr4-69202926;