2-100201157-T-G

Variant names:

• chr2-100201157-T-G
• rs10496345

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.297 in 152,124 control chromosomes in the GnomAD database, including 8,340 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 0.30 (8340 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.59

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 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: 0.297 AC: 45122 AN: 152006 Hom.: 8345 Cov.: 33

Gnomad AFR AF: 0.0804

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.297 AC: 45116 AN: 152124 Hom.: 8340 Cov.: 33 AF XY: 0.297 AC XY: 22081 AN XY: 74334

Gnomad4 AFR AF: 0.0801

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.307

Alfa AF: 0.310 Hom.: 1523

Bravo AF: 0.281

Asia WGS AF: 0.349 AC: 1212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	18
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496345; hg19: chr2-100817619;