rs4456706

Positions:

• chr2-240709406-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.725

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.455

Alfa AF: 0.390 Hom.: 3538

Bravo AF: 0.488

Asia WGS AF: 0.289 AC: 1008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4456706; hg19: chr2-241648823;