rs1357482

Positions:

• chr4-8494956-G-A

Variant summary

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

The ENST00000528132.1(ENSG00000205959):​n.170+12517G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0595 in 152,276 control chromosomes in the GnomAD database, including 494 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 0.060 (494 hom., cov: 32)
• Consequence: ENST00000528132.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRMT44	XM_047449679.1	c.2045-13842G>A		intron_variant
TRMT44	XM_047449680.1	c.2045-13842G>A		intron_variant
TRMT44	XM_047449681.1	c.2045-13842G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000528132.1	n.170+12517G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0594 AC: 9035 AN: 152158 Hom.: 488 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0300

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0190

Gnomad FIN AF: 0.0143

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0320

Gnomad OTH AF: 0.0574

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

GnomAD4 genome AF: 0.0595 AC: 9063 AN: 152276 Hom.: 494 Cov.: 32 AF XY: 0.0571 AC XY: 4249 AN XY: 74462

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.0300

Gnomad4 ASJ AF: 0.0239

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.0184

Gnomad4 FIN AF: 0.0143

Gnomad4 NFE AF: 0.0320

Gnomad4 OTH AF: 0.0568

Alfa AF: 0.0494 Hom.: 62

Bravo AF: 0.0643

Asia WGS AF: 0.0250 AC: 89 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.51
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1357482; hg19: chr4-8496683;