2-100201157-T-G

Variant names:

• chr2-100201157-T-G
• rs10496345

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0801 AC: 3329 AN: 41554

American (AMR) AF: 0.301 AC: 4597 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 907 AN: 3470

East Asian (EAS) AF: 0.560 AC: 2886 AN: 5158

South Asian (SAS) AF: 0.258 AC: 1243 AN: 4812

European-Finnish (FIN) AF: 0.413 AC: 4359 AN: 10550

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26852 AN: 67976

Other (OTH) AF: 0.307 AC: 650 AN: 2116

Alfa AF: 0.303 Hom.: 1523

Bravo AF: 0.281

Asia WGS AF: 0.349 AC: 1212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	18
DANN	Benign	0.82
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs10496345; hg19: chr2-100817619;