chr4-99323064-A-G

Variant names:

• chr4-99323064-A-G
• rs3811802

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 0.447 in 151,848 control chromosomes in the GnomAD database, including 15,752 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 0.45 (15752 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67832 AN: 151728 Hom.: 15744 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.0969

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.447 AC: 67869 AN: 151848 Hom.: 15752 Cov.: 32 AF XY: 0.443 AC XY: 32894 AN XY: 74220

African (AFR) AF: 0.500 AC: 20720 AN: 41402

American (AMR) AF: 0.372 AC: 5668 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1353 AN: 3466

East Asian (EAS) AF: 0.0965 AC: 498 AN: 5158

South Asian (SAS) AF: 0.294 AC: 1411 AN: 4800

European-Finnish (FIN) AF: 0.550 AC: 5804 AN: 10550

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31022 AN: 67922

Other (OTH) AF: 0.417 AC: 880 AN: 2112

Alfa AF: 0.432 Hom.: 20323

Bravo AF: 0.437

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.94
DANN	Benign	0.43
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs3811802; hg19: chr4-100244221;