rs1949733

chr4-8501632-A-Gchr4-8501632-A-T

Variant summary

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

The ENST00000528132.1(ENSG00000205959):n.171-7166A>G 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 0.737 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: ENST00000528132.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

Genes affected

(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/exons	MANE	UniProt
TRMT44	XM_047449679.1	c.2045-7166A>G		intron_variant
TRMT44	XM_047449680.1	c.2045-7166A>G		intron_variant
TRMT44	XM_047449681.1	c.2045-7166A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000528132.1	n.171-7166A>G		intron_variant, non_coding_transcript_variant		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;