rs1949733

Variant names:

• chr4-8501632-A-G
• rs1949733
• ENST00000528132.1:n.171-7166A>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

ENSG00000205959 (HGNC:):

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]

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRMT44	XM_047449679.1	c.2045-7166A>G		intron_variant	Intron 10 of 11		XP_047305635.1
TRMT44	XM_047449680.1	c.2045-7166A>G		intron_variant	Intron 10 of 12		XP_047305636.1
TRMT44	XM_047449681.1	c.2045-7166A>G		intron_variant	Intron 10 of 10		XP_047305637.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000205959	ENST00000528132.1	n.171-7166A>G		intron_variant	Intron 1 of 1	4

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 v4.3

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

Other links and lift over

dbSNP: rs1949733; hg19: chr4-8503359;