chr2-46659003-G-A

Variant names:

• chr2-46659003-G-A
• rs4953404

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 0.693 in 151,972 control chromosomes in the GnomAD database, including 36,843 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 0.69 (36843 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105252 AN: 151854 Hom.: 36820 Cov.: 30

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.693 AC: 105325 AN: 151972 Hom.: 36843 Cov.: 30 AF XY: 0.690 AC XY: 51264 AN XY: 74262

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.777

Gnomad4 ASJ AF: 0.739

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.673

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.710

Alfa AF: 0.700 Hom.: 4638

Bravo AF: 0.708

Asia WGS AF: 0.719 AC: 2501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4953404; hg19: chr2-46886142;