rs4456706

Variant names:

• chr2-240709406-A-G
• rs4456706

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 0.46 in 152,088 control chromosomes in the GnomAD database, including 18,424 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 0.46 (18424 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.27
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.718 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: 0.460 AC: 69860 AN: 151970 Hom.: 18387 Cov.: 32

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.460 AC: 69948 AN: 152088 Hom.: 18424 Cov.: 32 AF XY: 0.456 AC XY: 33903 AN XY: 74346

African (AFR) AF: 0.725 AC: 30059 AN: 41480

American (AMR) AF: 0.511 AC: 7809 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1746 AN: 3470

East Asian (EAS) AF: 0.249 AC: 1290 AN: 5176

South Asian (SAS) AF: 0.239 AC: 1152 AN: 4816

European-Finnish (FIN) AF: 0.334 AC: 3529 AN: 10578

Middle Eastern (MID) AF: 0.363 AC: 106 AN: 292

European-Non Finnish (NFE) AF: 0.337 AC: 22919 AN: 67982

Other (OTH) AF: 0.455 AC: 959 AN: 2110

Alfa AF: 0.390 Hom.: 5621

Bravo AF: 0.488

Asia WGS AF: 0.289 AC: 1008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.010
DANN	Benign	0.14
PhyloP100		-5.3

Splicing

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

Other links and lift over

dbSNP: rs4456706; hg19: chr2-241648823;