rs1386204

Variant names:

• chr4-45422446-A-G
• rs1386204

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 0.133 in 152,214 control chromosomes in the GnomAD database, including 2,380 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 (2380 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.312 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: 0.133 AC: 20228 AN: 152096 Hom.: 2347 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0886

Gnomad ASJ AF: 0.0827

Gnomad EAS AF: 0.0221

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0438

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0592

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.133 AC: 20307 AN: 152214 Hom.: 2380 Cov.: 32 AF XY: 0.131 AC XY: 9726 AN XY: 74434

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.0885

Gnomad4 ASJ AF: 0.0827

Gnomad4 EAS AF: 0.0222

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.0438

Gnomad4 NFE AF: 0.0593

Gnomad4 OTH AF: 0.108

Alfa AF: 0.107 Hom.: 196

Bravo AF: 0.142

Asia WGS AF: 0.111 AC: 385 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.6
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: rs1386204; hg19: chr4-45424463;