rs10183524

Variant names:

• chr2-120352302-G-A
• rs10183524

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;