chr2-100201157-T-G

Position:

• chr2-100201157-T-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;