rs386450

chr5-14106027-A-Gchr5-14106027-A-T

Variant summary

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

The variant allele was found at a frequency of 0.297 in 152,116 control chromosomes in the GnomAD database, including 7,946 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 0.30 (7946 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 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

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45192 AN: 151998 Hom.: 7932 Cov.: 32

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.297 AC: 45249 AN: 152116 Hom.: 7946 Cov.: 32 AF XY: 0.304 AC XY: 22576 AN XY: 74366

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.281

Alfa AF: 0.216 Hom.: 8091

Bravo AF: 0.306

Asia WGS AF: 0.455 AC: 1581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	10
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs386450; hg19: chr5-14106136;