2-223615542-A-G

Position:

• chr2-223615542-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 0.152 in 152,128 control chromosomes in the GnomAD database, including 3,298 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 0.15 (3298 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 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: 0.152 AC: 23049 AN: 152010 Hom.: 3279 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.0835

Gnomad ASJ AF: 0.0986

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.0657

Gnomad FIN AF: 0.0359

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.0581

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.152 AC: 23111 AN: 152128 Hom.: 3298 Cov.: 32 AF XY: 0.149 AC XY: 11081 AN XY: 74388

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.0833

Gnomad4 ASJ AF: 0.0986

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.0654

Gnomad4 FIN AF: 0.0359

Gnomad4 NFE AF: 0.0581

Gnomad4 OTH AF: 0.124

Alfa AF: 0.0928 Hom.: 718

Bravo AF: 0.165

Asia WGS AF: 0.108 AC: 375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.13
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs966414; hg19: chr2-224480259;