4-109882660-A-G

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 0.0686 in 152,282 control chromosomes in the GnomAD database, including 395 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 0.069 (395 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.175 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: 0.0685 AC: 10430 AN: 152164 Hom.: 393 Cov.: 31

Gnomad AFR AF: 0.0694

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.0813

Gnomad ASJ AF: 0.0806

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.0714

Gnomad FIN AF: 0.0496

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0579

Gnomad OTH AF: 0.0698

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

GnomAD4 genome AF: 0.0686 AC: 10451 AN: 152282 Hom.: 395 Cov.: 31 AF XY: 0.0703 AC XY: 5231 AN XY: 74460

Gnomad4 AFR AF: 0.0696

Gnomad4 AMR AF: 0.0809

Gnomad4 ASJ AF: 0.0806

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.0719

Gnomad4 FIN AF: 0.0496

Gnomad4 NFE AF: 0.0579

Gnomad4 OTH AF: 0.0738

Alfa AF: 0.0598 Hom.: 663

Bravo AF: 0.0709

Asia WGS AF: 0.127 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.6
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9685587; hg19: chr4-110803816;