rs4124163

Variant names:

• chr4-110824443-A-G
• rs4124163

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.201 AC: 8317 AN: 41476

American (AMR) AF: 0.0653 AC: 998 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0354 AC: 123 AN: 3472

East Asian (EAS) AF: 0.00252 AC: 13 AN: 5162

South Asian (SAS) AF: 0.0405 AC: 195 AN: 4818

European-Finnish (FIN) AF: 0.0372 AC: 395 AN: 10624

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0486 AC: 3307 AN: 68014

Other (OTH) AF: 0.0804 AC: 170 AN: 2114

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
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs4124163; hg19: chr4-111745599;