rs4790335

Variant names:

• chr17-2415401-G-A
• rs4790335
• ENST00000571332.5:n.685C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-2415401-G-A
• chr17-2415401-G-C
• chr17-2415401-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000571332.5(METTL16):​n.685C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 463,424 control chromosomes in the GnomAD database, including 114,461 homozygotes. 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: 𝑓 0.63 (31130 hom., cov: 26)
  • Exomes 𝑓: 0.72 (83331 hom.)
• Consequence: METTL16 ENST00000571332.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.90

Genes affected

METTL16 (HGNC:28484): (methyltransferase 16, RNA N6-adenosine) Enables RNA binding activity and RNA methyltransferase activity. Involved in RNA modification and regulation of mRNA metabolic process. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

LOC284009 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC284009	NR_028335.1	n.36C>T		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
METTL16	ENST00000571332.5	n.685C>T		non_coding_transcript_exon_variant	Exon 1 of 3	1
METTL16	ENST00000381977.3	n.136-154C>T		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.629 AC: 94435 AN: 150078 Hom.: 31108 Cov.: 26

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.834

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.637

GnomAD3 exomes AF: 0.721 AC: 150348 AN: 208594 Hom.: 55787 AF XY: 0.723 AC XY: 81936 AN XY: 113334

Gnomad AFR exome AF: 0.411

Gnomad AMR exome AF: 0.826

Gnomad ASJ exome AF: 0.700

Gnomad EAS exome AF: 0.976

Gnomad SAS exome AF: 0.826

Gnomad FIN exome AF: 0.737

Gnomad NFE exome AF: 0.664

Gnomad OTH exome AF: 0.708

GnomAD4 exome AF: 0.722 AC: 226304 AN: 313256 Hom.: 83331 Cov.: 0 AF XY: 0.730 AC XY: 129537 AN XY: 177478

Gnomad4 AFR exome AF: 0.423

Gnomad4 AMR exome AF: 0.825

Gnomad4 ASJ exome AF: 0.698

Gnomad4 EAS exome AF: 0.979

Gnomad4 SAS exome AF: 0.824

Gnomad4 FIN exome AF: 0.734

Gnomad4 NFE exome AF: 0.665

Gnomad4 OTH exome AF: 0.690

GnomAD4 genome AF: 0.629 AC: 94495 AN: 150168 Hom.: 31130 Cov.: 26 AF XY: 0.640 AC XY: 46895 AN XY: 73270

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.735

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.970

Gnomad4 SAS AF: 0.836

Gnomad4 FIN AF: 0.743

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.637

Alfa AF: 0.663 Hom.: 58391

Bravo AF: 0.618

Asia WGS AF: 0.836 AC: 2904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.10
DANN	Benign	0.63

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: rs4790335; hg19: chr17-2318695;