rs13416500

Variant names:

• chr2-200907075-A-G
• rs13416500

Your query was ambiguous. Multiple possible variants found:

• chr2-200907075-A-G
• chr2-200907075-A-T

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;