rs840203

Positions:

• chr4-45563705-A-G
• chr4-45563705-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 0.919 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.924

Gnomad4 AMR AF: 0.941

Gnomad4 ASJ AF: 0.875

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.917

Gnomad4 FIN AF: 0.924

Gnomad4 NFE AF: 0.906

Gnomad4 OTH AF: 0.916

Alfa AF: 0.915 Hom.: 7899

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs840203; hg19: chr4-45565722;