rs1949733

Variant names:

• chr4-8501632-A-G
• rs1949733
• XM_047449679.1:c.2045-7166A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-8501632-A-G
• chr4-8501632-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000528132.1(ENSG00000205959):​n.171-7166A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 152,082 control chromosomes in the GnomAD database, including 41,965 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 0.74 (41965 hom., cov: 31)
• Consequence: ENSG00000205959 ENST00000528132.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 26 publications found

Genes affected

TRMT44 (HGNC:26653): (tRNA methyltransferase 44 homolog) The protein encoded by this gene is a putative tRNA methyltransferase found in the cytoplasm. Defects in this gene may be a cause of partial epilepsy with pericentral spikes (PEPS), but that has not been proven definitively. [provided by RefSeq, May 2012]

ENSG00000205959 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000528132.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000205959	ENST00000528132.1	TSL:4	n.171-7166A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.737 AC: 111941 AN: 151964 Hom.: 41916 Cov.: 31

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.712

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.737 AC: 112040 AN: 152082 Hom.: 41965 Cov.: 31 AF XY: 0.733 AC XY: 54526 AN XY: 74348

African (AFR) AF: 0.857 AC: 35565 AN: 41500

American (AMR) AF: 0.617 AC: 9424 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2382 AN: 3468

East Asian (EAS) AF: 0.636 AC: 3269 AN: 5142

South Asian (SAS) AF: 0.849 AC: 4096 AN: 4824

European-Finnish (FIN) AF: 0.666 AC: 7047 AN: 10574

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.705 AC: 47928 AN: 67980

Other (OTH) AF: 0.714 AC: 1509 AN: 2112

Alfa AF: 0.707 Hom.: 131247

Bravo AF: 0.729

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.082
DANN	Benign	0.29
PhyloP100		-1.7

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1949733;

hg19: chr4-8503359;