4-109882660-A-G

Variant names:

• chr4-109882660-A-G
• rs9685587

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;