rs13398848

Variant names:

• chr2-84018044-A-G
• rs13398848

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.176 AC: 7322 AN: 41546

American (AMR) AF: 0.0616 AC: 941 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0311 AC: 108 AN: 3472

East Asian (EAS) AF: 0.0707 AC: 367 AN: 5188

South Asian (SAS) AF: 0.0257 AC: 124 AN: 4826

European-Finnish (FIN) AF: 0.0537 AC: 570 AN: 10614

Middle Eastern (MID) AF: 0.0548 AC: 16 AN: 292

European-Non Finnish (NFE) AF: 0.0233 AC: 1583 AN: 68018

Other (OTH) AF: 0.0700 AC: 148 AN: 2114

Alfa AF: 0.0394 Hom.: 763

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
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs13398848; hg19: chr2-84245168;