3-133745840-G-A

Position:

• chr3-133745840-G-A

Variant summary

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

The ENST00000460564.5(ENSG00000291042):​n.382-7755G>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 0.406 in 155,178 control chromosomes in the GnomAD database, including 13,240 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 0.41 (13089 hom., cov: 32)
  • Exomes 𝑓: 0.27 (151 hom.)
• Consequence: ENST00000460564.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.596

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TF	NM_001354703.2	c.-89-2572G>A		intron_variant			NP_001341632.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000460564.5	n.382-7755G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62158 AN: 151894 Hom.: 13071 Cov.: 32

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.370

GnomAD4 exome AF: 0.268 AC: 847 AN: 3166 Hom.: 151 AF XY: 0.268 AC XY: 424 AN XY: 1582

Gnomad4 AFR exome AF: 0.467

Gnomad4 AMR exome AF: 0.293

Gnomad4 ASJ exome AF: 0.357

Gnomad4 EAS exome AF: 0.400

Gnomad4 SAS exome AF: 0.285

Gnomad4 FIN exome AF: 0.271

Gnomad4 NFE exome AF: 0.252

Gnomad4 OTH exome AF: 0.254

GnomAD4 genome AF: 0.409 AC: 62225 AN: 152012 Hom.: 13089 Cov.: 32 AF XY: 0.412 AC XY: 30571 AN XY: 74284

Gnomad4 AFR AF: 0.478

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.370

Alfa AF: 0.397 Hom.: 1967

Bravo AF: 0.414

Asia WGS AF: 0.511 AC: 1777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.3
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4481157; hg19: chr3-133464684;