chr3-183885037-A-G

Position:

• chr3-183885037-A-G

Variant summary

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

The ENST00000445165.1(ENSG00000293259):​n.114A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 982,496 control chromosomes in the GnomAD database, including 13,790 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 0.13 (1852 hom., cov: 33)
  • Exomes 𝑓: 0.15 (11938 hom.)
• Consequence: ENST00000445165.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.75

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000445165.1	n.114A>G		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19687 AN: 151854 Hom.: 1838 Cov.: 33

Gnomad AFR AF: 0.0410

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.0943

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.130

GnomAD4 exome AF: 0.149 AC: 123965 AN: 830524 Hom.: 11938 Cov.: 11 AF XY: 0.152 AC XY: 63779 AN XY: 419834

Gnomad4 AFR exome AF: 0.0380

Gnomad4 AMR exome AF: 0.225

Gnomad4 ASJ exome AF: 0.100

Gnomad4 EAS exome AF: 0.457

Gnomad4 SAS exome AF: 0.244

Gnomad4 FIN exome AF: 0.194

Gnomad4 NFE exome AF: 0.123

Gnomad4 OTH exome AF: 0.150

GnomAD4 genome AF: 0.130 AC: 19714 AN: 151972 Hom.: 1852 Cov.: 33 AF XY: 0.137 AC XY: 10196 AN XY: 74280

Gnomad4 AFR AF: 0.0411

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.0943

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.139

Alfa AF: 0.115 Hom.: 151

Bravo AF: 0.124

Asia WGS AF: 0.360 AC: 1249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3792589; hg19: chr3-183602825; COSMIC: COSV57699842;