chr4-66435084-A-G

Variant names:

• chr4-66435084-A-G
• rs2009314

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 0.328 in 151,910 control chromosomes in the GnomAD database, including 9,983 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 0.33 (9983 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.568 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: 0.328 AC: 49716 AN: 151792 Hom.: 9959 Cov.: 31

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.328 AC: 49787 AN: 151910 Hom.: 9983 Cov.: 31 AF XY: 0.327 AC XY: 24284 AN XY: 74230

African (AFR) AF: 0.574 AC: 23769 AN: 41396

American (AMR) AF: 0.287 AC: 4385 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 678 AN: 3470

East Asian (EAS) AF: 0.286 AC: 1468 AN: 5134

South Asian (SAS) AF: 0.247 AC: 1187 AN: 4810

European-Finnish (FIN) AF: 0.260 AC: 2746 AN: 10572

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14795 AN: 67954

Other (OTH) AF: 0.280 AC: 590 AN: 2108

Alfa AF: 0.255 Hom.: 17709

Bravo AF: 0.340

Asia WGS AF: 0.258 AC: 899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.93
DANN	Benign	0.43
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2009314; hg19: chr4-67300802;