chr3-133717292-C-A

Position:

• chr3-133717292-C-A

Variant summary

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

The ENST00000460564.5(ENSG00000291042):​n.381+16239C>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 0.324 in 151,954 control chromosomes in the GnomAD database, including 8,196 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 0.32 (8196 hom., cov: 31)
• Consequence: ENST00000460564.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TF	NM_001354703.2	c.-90+4111C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000460564.5	n.381+16239C>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49191 AN: 151836 Hom.: 8194 Cov.: 31

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.324 AC: 49218 AN: 151954 Hom.: 8196 Cov.: 31 AF XY: 0.326 AC XY: 24211 AN XY: 74254

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.301

Alfa AF: 0.315 Hom.: 15539

Bravo AF: 0.327

Asia WGS AF: 0.432 AC: 1501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4525863; hg19: chr3-133436136; COSMIC: COSV71704636;