rs4404064

Variant names:

• chr16-82019894-G-A
• rs4404064

Your query was ambiguous. Multiple possible variants found:

• chr16-82019894-G-A
• chr16-82019894-G-C
• chr16-82019894-G-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 0.95 in 152,338 control chromosomes in the GnomAD database, including 68,823 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 0.95 (68823 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.89
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.978 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.950 AC: 144583 AN: 152220 Hom.: 68761 Cov.: 32

Gnomad AFR AF: 0.986

Gnomad AMI AF: 0.956

Gnomad AMR AF: 0.957

Gnomad ASJ AF: 0.900

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.939

Gnomad FIN AF: 0.944

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.928

Gnomad OTH AF: 0.941

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

GnomAD4 genome AF: 0.950 AC: 144705 AN: 152338 Hom.: 68823 Cov.: 32 AF XY: 0.950 AC XY: 70760 AN XY: 74486

African (AFR) AF: 0.986 AC: 40984 AN: 41582

American (AMR) AF: 0.957 AC: 14646 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.900 AC: 3125 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5156 AN: 5172

South Asian (SAS) AF: 0.938 AC: 4527 AN: 4826

European-Finnish (FIN) AF: 0.944 AC: 10023 AN: 10618

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.928 AC: 63116 AN: 68040

Other (OTH) AF: 0.942 AC: 1991 AN: 2114

Alfa AF: 0.932 Hom.: 38950

Bravo AF: 0.953

Asia WGS AF: 0.971 AC: 3378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.014
DANN	Benign	0.61
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs4404064; hg19: chr16-82053499;