rs4124163

chr4-110824443-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 0.0895 in 152,164 control chromosomes in the GnomAD database, including 1,001 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 0.090 (1001 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 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: 0.0894 AC: 13595 AN: 152046 Hom.: 998 Cov.: 31

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0655

Gnomad ASJ AF: 0.0354

Gnomad EAS AF: 0.00232

Gnomad SAS AF: 0.0404

Gnomad FIN AF: 0.0372

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0486

Gnomad OTH AF: 0.0813

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

GnomAD4 genome AF: 0.0895 AC: 13619 AN: 152164 Hom.: 1001 Cov.: 31 AF XY: 0.0863 AC XY: 6423 AN XY: 74384

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.0653

Gnomad4 ASJ AF: 0.0354

Gnomad4 EAS AF: 0.00252

Gnomad4 SAS AF: 0.0405

Gnomad4 FIN AF: 0.0372

Gnomad4 NFE AF: 0.0486

Gnomad4 OTH AF: 0.0804

Alfa AF: 0.0654 Hom.: 92

Bravo AF: 0.0973

Asia WGS AF: 0.0400 AC: 141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.3
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4124163; hg19: chr4-111745599;