chr2-224082453-A-G

Position:

• chr2-224082453-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 0.135 in 152,272 control chromosomes in the GnomAD database, including 1,593 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 0.13 (1593 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20536 AN: 152154 Hom.: 1592 Cov.: 32

Gnomad AFR AF: 0.0580

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.135 AC: 20531 AN: 152272 Hom.: 1593 Cov.: 32 AF XY: 0.135 AC XY: 10066 AN XY: 74448

Gnomad4 AFR AF: 0.0579

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.154

Alfa AF: 0.144 Hom.: 214

Bravo AF: 0.133

Asia WGS AF: 0.182 AC: 633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16865545; hg19: chr2-224947170;