chr2-221196620-C-G

Variant names:

• chr2-221196620-C-G
• rs715021

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 0.255 in 151,646 control chromosomes in the GnomAD database, including 5,087 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 0.25 (5087 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.318 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: 0.255 AC: 38596 AN: 151528 Hom.: 5075 Cov.: 30

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.255 AC: 38645 AN: 151646 Hom.: 5087 Cov.: 30 AF XY: 0.260 AC XY: 19230 AN XY: 74054

African (AFR) AF: 0.294 AC: 12164 AN: 41356

American (AMR) AF: 0.326 AC: 4961 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 735 AN: 3460

East Asian (EAS) AF: 0.184 AC: 945 AN: 5130

South Asian (SAS) AF: 0.204 AC: 979 AN: 4806

European-Finnish (FIN) AF: 0.286 AC: 2985 AN: 10442

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.220 AC: 14952 AN: 67908

Other (OTH) AF: 0.242 AC: 510 AN: 2104

Alfa AF: 0.144 Hom.: 266

Bravo AF: 0.258

Asia WGS AF: 0.190 AC: 660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.52
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs715021; hg19: chr2-222061340;