rs386450

Variant names:

• chr5-14106027-A-G
• rs386450

Your query was ambiguous. Multiple possible variants found:

• chr5-14106027-A-G
• chr5-14106027-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.460 AC: 19078 AN: 41486

American (AMR) AF: 0.257 AC: 3937 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 751 AN: 3468

East Asian (EAS) AF: 0.555 AC: 2870 AN: 5174

South Asian (SAS) AF: 0.354 AC: 1706 AN: 4818

European-Finnish (FIN) AF: 0.248 AC: 2624 AN: 10584

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.198 AC: 13438 AN: 67984

Other (OTH) AF: 0.281 AC: 592 AN: 2106

Alfa AF: 0.234 Hom.: 13900

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
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs386450; hg19: chr5-14106136;