chr3-133744613-G-A

Position:

• chr3-133744613-G-A

Variant summary

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

The ENST00000460564.5(ENSG00000291042):​n.382-8982G>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 0.584 in 151,960 control chromosomes in the GnomAD database, including 26,455 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 0.58 (26455 hom., cov: 32)
• Consequence: ENST00000460564.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TF	NM_001354703.2	c.-89-3799G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000460564.5	n.382-8982G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88709 AN: 151842 Hom.: 26416 Cov.: 32

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.584 AC: 88800 AN: 151960 Hom.: 26455 Cov.: 32 AF XY: 0.586 AC XY: 43499 AN XY: 74272

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.637

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.759

Gnomad4 SAS AF: 0.702

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.556

Alfa AF: 0.571 Hom.: 3494

Bravo AF: 0.597

Asia WGS AF: 0.756 AC: 2629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.17
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8177179; hg19: chr3-133463457;