rs10153799

Positions:

• chr2-57552907-T-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 0.0773 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;