4-39669522-G-A

Variant names:

• chr4-39669522-G-A
• rs1484322

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 0.3 in 151,994 control chromosomes in the GnomAD database, including 8,157 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 0.30 (8157 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45557 AN: 151876 Hom.: 8146 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.300 AC: 45575 AN: 151994 Hom.: 8157 Cov.: 32 AF XY: 0.298 AC XY: 22126 AN XY: 74286

African (AFR) AF: 0.100 AC: 4155 AN: 41474

American (AMR) AF: 0.465 AC: 7090 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1146 AN: 3472

East Asian (EAS) AF: 0.407 AC: 2098 AN: 5150

South Asian (SAS) AF: 0.376 AC: 1814 AN: 4820

European-Finnish (FIN) AF: 0.273 AC: 2878 AN: 10550

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25220 AN: 67964

Other (OTH) AF: 0.353 AC: 744 AN: 2108

Alfa AF: 0.348 Hom.: 27975

Bravo AF: 0.304

Asia WGS AF: 0.386 AC: 1342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	11
DANN	Benign	0.85
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs1484322; hg19: chr4-39671142;