2-655222-G-A

Variant names:

• chr2-655222-G-A
• rs13029479

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 0.128 in 152,308 control chromosomes in the GnomAD database, including 1,369 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 (1369 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 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: 0.128 AC: 19469 AN: 152190 Hom.: 1368 Cov.: 34

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.0606

Gnomad SAS AF: 0.0775

Gnomad FIN AF: 0.0948

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.128 AC: 19491 AN: 152308 Hom.: 1369 Cov.: 34 AF XY: 0.126 AC XY: 9393 AN XY: 74470

African (AFR) AF: 0.170 AC: 7058 AN: 41558

American (AMR) AF: 0.107 AC: 1642 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 860 AN: 3472

East Asian (EAS) AF: 0.0603 AC: 313 AN: 5188

South Asian (SAS) AF: 0.0778 AC: 375 AN: 4822

European-Finnish (FIN) AF: 0.0948 AC: 1007 AN: 10620

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7710 AN: 68030

Other (OTH) AF: 0.134 AC: 283 AN: 2112

Alfa AF: 0.119 Hom.: 2605

Bravo AF: 0.133

Asia WGS AF: 0.0810 AC: 279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.53
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs13029479; hg19: chr2-655222;