chr4-106384408-G-A

Position:

• chr4-106384408-G-A

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 0.369 in 150,884 control chromosomes in the GnomAD database, including 11,271 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 0.37 (11271 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.106384408G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.369 AC: 55574 AN: 150772 Hom.: 11256 Cov.: 30

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.369 AC: 55632 AN: 150884 Hom.: 11271 Cov.: 30 AF XY: 0.365 AC XY: 26904 AN XY: 73626

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.365

Alfa AF: 0.326 Hom.: 1500

Bravo AF: 0.378

Asia WGS AF: 0.291 AC: 1000 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.9
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2949632; hg19: chr4-107305565;