rs10496384

chr2-104353103-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 0.0963 in 149,826 control chromosomes in the GnomAD database, including 2,015 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 0.096 (2015 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.903

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0961 AC: 14385 AN: 149736 Hom.: 2010 Cov.: 28

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0813

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.0513

Gnomad SAS AF: 0.0143

Gnomad FIN AF: 0.00259

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.00535

Gnomad OTH AF: 0.0719

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

GnomAD4 genome AF: 0.0963 AC: 14426 AN: 149826 Hom.: 2015 Cov.: 28 AF XY: 0.0937 AC XY: 6844 AN XY: 73076

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.0813

Gnomad4 ASJ AF: 0.0127

Gnomad4 EAS AF: 0.0516

Gnomad4 SAS AF: 0.0141

Gnomad4 FIN AF: 0.00259

Gnomad4 NFE AF: 0.00535

Gnomad4 OTH AF: 0.0743

Alfa AF: 0.0436 Hom.: 161

Bravo AF: 0.114

Asia WGS AF: 0.0680 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.11
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496384; hg19: chr2-104969561;