rs840203

Variant names:

• chr4-45563705-A-G
• rs840203

Your query was ambiguous. Multiple possible variants found:

• chr4-45563705-A-G
• chr4-45563705-A-T

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 0.919 in 152,196 control chromosomes in the GnomAD database, including 64,263 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 0.92 (64263 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.919 AC: 139706 AN: 152078 Hom.: 64207 Cov.: 34

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.941

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.924

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.914

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

GnomAD4 genome AF: 0.919 AC: 139822 AN: 152196 Hom.: 64263 Cov.: 34 AF XY: 0.920 AC XY: 68472 AN XY: 74400

African (AFR) AF: 0.924 AC: 38393 AN: 41548

American (AMR) AF: 0.941 AC: 14398 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3033 AN: 3466

East Asian (EAS) AF: 0.999 AC: 5179 AN: 5186

South Asian (SAS) AF: 0.917 AC: 4433 AN: 4832

European-Finnish (FIN) AF: 0.924 AC: 9800 AN: 10606

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.906 AC: 61537 AN: 67940

Other (OTH) AF: 0.916 AC: 1930 AN: 2108

Alfa AF: 0.915 Hom.: 8227

Bravo AF: 0.922

Asia WGS AF: 0.969 AC: 3365 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.67
DANN	Benign	0.79
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs840203; hg19: chr4-45565722;