rs10153799

Variant names:

• chr2-57552907-T-G
• rs10153799

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 0.0773 in 151,928 control chromosomes in the GnomAD database, including 1,049 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 0.077 (1049 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 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: 0.0772 AC: 11719 AN: 151810 Hom.: 1048 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0506

Gnomad ASJ AF: 0.0586

Gnomad EAS AF: 0.0794

Gnomad SAS AF: 0.0622

Gnomad FIN AF: 0.0112

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0137

Gnomad OTH AF: 0.0810

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

GnomAD4 genome AF: 0.0773 AC: 11737 AN: 151928 Hom.: 1049 Cov.: 32 AF XY: 0.0763 AC XY: 5669 AN XY: 74268

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.0504

Gnomad4 ASJ AF: 0.0586

Gnomad4 EAS AF: 0.0788

Gnomad4 SAS AF: 0.0622

Gnomad4 FIN AF: 0.0112

Gnomad4 NFE AF: 0.0137

Gnomad4 OTH AF: 0.0802

Alfa AF: 0.0526 Hom.: 89

Bravo AF: 0.0842

Asia WGS AF: 0.0680 AC: 236 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.1
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10153799; hg19: chr2-57780042;