rs4439928

Variant names:

• chr2-170863055-A-G
• rs4439928

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 0.105 in 152,134 control chromosomes in the GnomAD database, including 892 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 0.11 (892 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.395
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.158 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: 0.105 AC: 16034 AN: 152016 Hom.: 893 Cov.: 30

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0757

Gnomad ASJ AF: 0.0859

Gnomad EAS AF: 0.0622

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0973

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

GnomAD4 genome AF: 0.105 AC: 16029 AN: 152134 Hom.: 892 Cov.: 30 AF XY: 0.106 AC XY: 7855 AN XY: 74400

African (AFR) AF: 0.100 AC: 4158 AN: 41494

American (AMR) AF: 0.0756 AC: 1157 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0859 AC: 298 AN: 3468

East Asian (EAS) AF: 0.0618 AC: 320 AN: 5180

South Asian (SAS) AF: 0.167 AC: 806 AN: 4812

European-Finnish (FIN) AF: 0.131 AC: 1391 AN: 10580

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7621 AN: 67988

Other (OTH) AF: 0.0958 AC: 202 AN: 2108

Alfa AF: 0.109 Hom.: 1147

Bravo AF: 0.0971

Asia WGS AF: 0.0930 AC: 323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.5
DANN	Benign	0.38
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs4439928; hg19: chr2-171719565;