rs3792588

chr3-183885043-C-G

Variant summary

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

The ENST00000445165.1(ENSG00000293259):n.120C>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 0.145 in 945,084 control chromosomes in the GnomAD database, including 13,430 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 (1844 hom., cov: 33)
  • Exomes 𝑓: 0.15 (11586 hom.)
• Consequence: ENST00000445165.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000445165.1	n.120C>G		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19392 AN: 152066 Hom.: 1830 Cov.: 33

Gnomad AFR AF: 0.0341

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.0926

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.129

GnomAD4 exome AF: 0.148 AC: 117593 AN: 792900 Hom.: 11586 Cov.: 10 AF XY: 0.151 AC XY: 60754 AN XY: 401532

Gnomad4 AFR exome AF: 0.0303

Gnomad4 AMR exome AF: 0.232

Gnomad4 ASJ exome AF: 0.100

Gnomad4 EAS exome AF: 0.456

Gnomad4 SAS exome AF: 0.245

Gnomad4 FIN exome AF: 0.195

Gnomad4 NFE exome AF: 0.120

Gnomad4 OTH exome AF: 0.149

GnomAD4 genome AF: 0.128 AC: 19420 AN: 152184 Hom.: 1844 Cov.: 33 AF XY: 0.135 AC XY: 10050 AN XY: 74398

Gnomad4 AFR AF: 0.0342

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.0926

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.137

Alfa AF: 0.118 Hom.: 155

Bravo AF: 0.122

Asia WGS AF: 0.359 AC: 1247 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	0.52
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3792588; hg19: chr3-183602831; COSMIC: COSV57699844;