chr3-133718757-C-T

Position:

• chr3-133718757-C-T

Variant summary

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

The ENST00000460564.5(ENSG00000291042):​n.381+17704C>T 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 0.0899 in 152,156 control chromosomes in the GnomAD database, including 829 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 0.090 (829 hom., cov: 32)
• Consequence: ENST00000460564.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TF	NM_001354703.2	c.-90+5576C>T		intron_variant			NP_001341632.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000460564.5	n.381+17704C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0897 AC: 13637 AN: 152038 Hom.: 820 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0210

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0519

Gnomad OTH AF: 0.0924

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

GnomAD4 genome AF: 0.0899 AC: 13673 AN: 152156 Hom.: 829 Cov.: 32 AF XY: 0.0900 AC XY: 6696 AN XY: 74378

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.0620

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.0210

Gnomad4 NFE AF: 0.0519

Gnomad4 OTH AF: 0.0986

Alfa AF: 0.0738 Hom.: 123

Bravo AF: 0.100

Asia WGS AF: 0.196 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16840699; hg19: chr3-133437601;