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. The variant received -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
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000571332.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC284009	NR_028335.1		n.36C>T		non_coding_transcript_exon	Exon 1 of 3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	METTL16	ENST00000571332.5	TSL:1	n.685C>T		non_coding_transcript_exon	Exon 1 of 3
	METTL16	ENST00000381977.3	TSL:4	n.136-154C>T		intron	N/A

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

GnomAD2 exomes AF: 0.721 AC: 150348 AN: 208594 AF XY: 0.723

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 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

African (AFR) AF: 0.423 AC: 3546 AN: 8388

American (AMR) AF: 0.825 AC: 25919 AN: 31398

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 6091 AN: 8724

East Asian (EAS) AF: 0.979 AC: 11226 AN: 11470

South Asian (SAS) AF: 0.824 AC: 47291 AN: 57420

European-Finnish (FIN) AF: 0.734 AC: 17953 AN: 24458

Middle Eastern (MID) AF: 0.662 AC: 1712 AN: 2588

European-Non Finnish (NFE) AF: 0.665 AC: 103127 AN: 155124

Other (OTH) AF: 0.690 AC: 9439 AN: 13686

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

African (AFR) AF: 0.422 AC: 17111 AN: 40566

American (AMR) AF: 0.735 AC: 11048 AN: 15026

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2420 AN: 3464

East Asian (EAS) AF: 0.970 AC: 4974 AN: 5126

South Asian (SAS) AF: 0.836 AC: 3982 AN: 4766

European-Finnish (FIN) AF: 0.743 AC: 7599 AN: 10226

Middle Eastern (MID) AF: 0.691 AC: 199 AN: 288

European-Non Finnish (NFE) AF: 0.666 AC: 45106 AN: 67734

Other (OTH) AF: 0.637 AC: 1317 AN: 2066

Alfa AF: 0.651 Hom.: 98819

Bravo AF: 0.618

Asia WGS AF: 0.836 AC: 2904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.10
DANN	Benign	0.63
PhyloP100		-3.9

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

Other links and lift over

dbSNP: rs4790335; hg19: chr17-2318695;