rs10183524

chr2-120352302-G-A

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 0.0843 in 152,170 control chromosomes in the GnomAD database, including 842 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 0.084 (842 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.189 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: 0.0842 AC: 12809 AN: 152052 Hom.: 835 Cov.: 33

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0496

Gnomad ASJ AF: 0.0534

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.0419

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.0402

Gnomad OTH AF: 0.0623

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

GnomAD4 genome AF: 0.0843 AC: 12834 AN: 152170 Hom.: 842 Cov.: 33 AF XY: 0.0867 AC XY: 6453 AN XY: 74412

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.0495

Gnomad4 ASJ AF: 0.0534

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.0419

Gnomad4 NFE AF: 0.0402

Gnomad4 OTH AF: 0.0659

Alfa AF: 0.0569 Hom.: 47

Bravo AF: 0.0843

Asia WGS AF: 0.229 AC: 795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.041
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10183524; hg19: chr2-121109878;