rs5817153

Variant names:

• chr16-58543411-GAAAAAA-G
• ENST00000441024.6:c.4624_4629delTTTTTT

Your query was ambiguous. Multiple possible variants found:

• chr16-58543411-GAAAAAA-G
• chr16-58543411-GAAAAAA-GAA
• chr16-58543411-GAAAAAA-GAAA
• chr16-58543411-GAAAAAA-GAAAA
• chr16-58543411-GAAAAAA-GAAAAA
• chr16-58543411-GAAAAAA-GAAAAAAA
• chr16-58543411-GAAAAAA-GAAAAAAAA
• chr16-58543411-GAAAAAA-GAAAAAAAAA
• chr16-58543411-GAAAAAA-GAAAAAAAAAA
• chr16-58543411-GAAAAAA-GAAAAAAAAAAAAAAAA

Variant summary

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

The NM_206999.3(CNOT1):​c.4624_4629delTTTTTT​(p.Phe1542_Phe1543del) variant causes a conservative inframe deletion change. The variant allele was found at a frequency of 0.000000821 in 1,218,550 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: 21)
  • Exomes 𝑓: 8.2e-7 (0 hom.)
• Consequence: CNOT1 NM_206999.3 conservative_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.77

Genes affected

CNOT1 (HGNC:7877): (CCR4-NOT transcription complex subunit 1) Enables armadillo repeat domain binding activity; molecular adaptor activity; and nuclear receptor binding activity. Contributes to poly(A)-specific ribonuclease activity. Involved in several processes, including negative regulation of signal transduction; positive regulation of cytoplasmic mRNA processing body assembly; and regulation of gene expression. Located in P-body and cytosol. Part of CCR4-NOT complex. Implicated in holoprosencephaly. [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
CNOT1	NM_016284.5	c.4434+190_4434+195delTTTTTT		intron_variant	Intron 31 of 48	ENST00000317147.10	NP_057368.3
CNOT1	NM_206999.3	c.4624_4629delTTTTTT	p.Phe1542_Phe1543del	conservative_inframe_deletion	Exon 31 of 31		NP_996882.1
CNOT1	NM_001265612.2	c.4419+190_4419+195delTTTTTT		intron_variant	Intron 31 of 48		NP_001252541.1
CNOT1	NR_049763.2	n.4692+190_4692+195delTTTTTT		intron_variant	Intron 31 of 49

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNOT1	ENST00000317147.10	c.4434+190_4434+195delTTTTTT		intron_variant	Intron 31 of 48	1	NM_016284.5	ENSP00000320949.5

Frequencies

GnomAD3 genomes Cov.: 21

GnomAD4 exome AF: 8.21e-7 AC: 1 AN: 1218550 Hom.: 0 AF XY: 0.00000168 AC XY: 1 AN XY: 594676

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: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000104

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 21

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr16-58577315;