rs4371699

Variant names:

• chr4-141579900-A-C
• rs4371699

Your query was ambiguous. Multiple possible variants found:

• chr4-141579900-A-C
• chr4-141579900-A-G
• chr4-141579900-A-T

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 0.855 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.933

Gnomad4 AMR AF: 0.867

Gnomad4 ASJ AF: 0.829

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.905

Gnomad4 FIN AF: 0.775

Gnomad4 NFE AF: 0.806

Gnomad4 OTH AF: 0.836

Alfa AF: 0.812 Hom.: 62095

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4371699; hg19: chr4-142501053;