rs13416500

chr2-200907075-A-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 0.232 in 148,168 control chromosomes in the GnomAD database, including 4,611 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 0.23 (4611 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.232 AC: 34324 AN: 148036 Hom.: 4603 Cov.: 30

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.00928

Gnomad SAS AF: 0.0836

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.163

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.232 AC: 34374 AN: 148168 Hom.: 4611 Cov.: 30 AF XY: 0.227 AC XY: 16461 AN XY: 72480

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.00930

Gnomad4 SAS AF: 0.0837

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.223

Alfa AF: 0.217 Hom.: 524

Bravo AF: 0.236

Asia WGS AF: 0.0730 AC: 256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	2.4
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13416500; hg19: chr2-201771798;