rs4953404

Positions:

• chr2-46659003-G-A
• chr2-46659003-G-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;