4-141579900-A-C

Variant names:

• chr4-141579900-A-C
• rs4371699

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 0.855 in 151,992 control chromosomes in the GnomAD database, including 55,872 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 0.86 (55872 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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: 0.855 AC: 129832 AN: 151874 Hom.: 55804 Cov.: 31

Gnomad AFR AF: 0.933

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.905

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.780

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.834

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

GnomAD4 genome AF: 0.855 AC: 129958 AN: 151992 Hom.: 55872 Cov.: 31 AF XY: 0.856 AC XY: 63590 AN XY: 74282

African (AFR) AF: 0.933 AC: 38725 AN: 41526

American (AMR) AF: 0.867 AC: 13225 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2877 AN: 3470

East Asian (EAS) AF: 0.994 AC: 5125 AN: 5156

South Asian (SAS) AF: 0.905 AC: 4359 AN: 4816

European-Finnish (FIN) AF: 0.775 AC: 8155 AN: 10524

Middle Eastern (MID) AF: 0.784 AC: 229 AN: 292

European-Non Finnish (NFE) AF: 0.806 AC: 54778 AN: 67940

Other (OTH) AF: 0.836 AC: 1765 AN: 2110

Alfa AF: 0.814 Hom.: 71935

Bravo AF: 0.863

Asia WGS AF: 0.922 AC: 3200 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.42
PhyloP100		-0.054

Splicing

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

Other links and lift over

dbSNP: rs4371699; hg19: chr4-142501053;