7-73840121-CTGTG-CTGTGTGTG

Variant names:

• chr7-73840121-C-CTGTG
• rs375025208
• NM_152559.3:c.389-5_389-2dupCACA

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_Strong PM2

The NM_152559.3(METTL27):​c.389-5_389-2dupCACA variant causes a splice acceptor, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 27)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: METTL27 NM_152559.3 splice_acceptor, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.12

Genes affected

METTL27 (HGNC:19068): (methyltransferase like 27) This gene encodes a protein belonging to ubiE/COQ5 methyltransferase family. The gene is deleted in Williams syndrome, a multisystem developmental disorder caused by the deletion of contiguous genes at 7q11.22-q11.23. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.12195122 fraction of the gene. No cryptic splice site detected. Exon removal is inframe change.
• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
METTL27	NM_152559.3	c.389-5_389-2dupCACA		splice_acceptor_variant, intron_variant	Intron 4 of 5	ENST00000297873.9	NP_689772.2
METTL27	XM_017011777.2	c.389-5_389-2dupCACA		splice_acceptor_variant, intron_variant	Intron 4 of 5		XP_016867266.1
METTL27	XM_017011778.2	c.389-5_389-2dupCACA		splice_acceptor_variant, intron_variant	Intron 4 of 5		XP_016867267.1
METTL27	XR_001744563.2	n.420-5_420-2dupCACA		splice_acceptor_variant, intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
METTL27	ENST00000297873.9	c.389-2_389-1insCACA		splice_acceptor_variant, intron_variant	Intron 4 of 5	1	NM_152559.3	ENSP00000297873.4
METTL27	ENST00000458679.5	n.253-2_253-1insCACA		splice_acceptor_variant, intron_variant	Intron 3 of 4	4		ENSP00000398533.1
METTL27	ENST00000493174.1	n.284-2_284-1insCACA		splice_acceptor_variant, intron_variant	Intron 3 of 3	2

Frequencies

GnomAD3 genomes Cov.: 27

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1350360 Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0 AN XY: 669174

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: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 27

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: rs375025208; hg19: chr7-73254451;