rs13404596

chr2-200907078-T-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 0.234 in 146,912 control chromosomes in the GnomAD database, including 4,608 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 (4608 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.378 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: 0.234 AC: 34309 AN: 146778 Hom.: 4600 Cov.: 30

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.00956

Gnomad SAS AF: 0.0848

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.234 AC: 34359 AN: 146912 Hom.: 4608 Cov.: 30 AF XY: 0.229 AC XY: 16447 AN XY: 71718

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.00959

Gnomad4 SAS AF: 0.0848

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.227

Alfa AF: 0.217 Hom.: 523

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	-0.85
Cadd	Benign	1.1
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13404596; hg19: chr2-201771801;