rs13398848

chr2-84018044-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 0.0734 in 152,270 control chromosomes in the GnomAD database, including 797 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 0.073 (797 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.684

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 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: 0.0732 AC: 11142 AN: 152152 Hom.: 788 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0618

Gnomad ASJ AF: 0.0311

Gnomad EAS AF: 0.0710

Gnomad SAS AF: 0.0261

Gnomad FIN AF: 0.0537

Gnomad MID AF: 0.0541

Gnomad NFE AF: 0.0233

Gnomad OTH AF: 0.0717

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

GnomAD4 genome AF: 0.0734 AC: 11180 AN: 152270 Hom.: 797 Cov.: 32 AF XY: 0.0736 AC XY: 5482 AN XY: 74464

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.0616

Gnomad4 ASJ AF: 0.0311

Gnomad4 EAS AF: 0.0707

Gnomad4 SAS AF: 0.0257

Gnomad4 FIN AF: 0.0537

Gnomad4 NFE AF: 0.0233

Gnomad4 OTH AF: 0.0700

Alfa AF: 0.0317 Hom.: 167

Bravo AF: 0.0781

Asia WGS AF: 0.0520 AC: 179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.6
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13398848; hg19: chr2-84245168;