chr4-8501632-A-G

Variant names:

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

Variant summary

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

The XM_047449679.1(TRMT44):​c.2045-7166A>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: TRMT44 XM_047449679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

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

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.857

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.849

Gnomad4 FIN AF: 0.666

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.714

Alfa AF: 0.699 Hom.: 84072

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1949733; hg19: chr4-8503359;