4-186067699-A-T

Position:

• chr4-186067699-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 0.176 in 152,184 control chromosomes in the GnomAD database, including 2,473 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 0.18 (2473 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26738 AN: 152066 Hom.: 2469 Cov.: 33

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.176 AC: 26768 AN: 152184 Hom.: 2473 Cov.: 33 AF XY: 0.176 AC XY: 13081 AN XY: 74390

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.175

Alfa AF: 0.179 Hom.: 328

Bravo AF: 0.173

Asia WGS AF: 0.177 AC: 614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.29
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5743303; hg19: chr4-186988853;