chr2-206388916-A-G

Variant names:

• chr2-206388916-A-G
• rs1448901

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 0.207 in 152,208 control chromosomes in the GnomAD database, including 3,680 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 0.21 (3680 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31497 AN: 152090 Hom.: 3677 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.207 AC: 31514 AN: 152208 Hom.: 3680 Cov.: 32 AF XY: 0.205 AC XY: 15249 AN XY: 74416

African (AFR) AF: 0.103 AC: 4294 AN: 41556

American (AMR) AF: 0.199 AC: 3044 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 733 AN: 3472

East Asian (EAS) AF: 0.187 AC: 966 AN: 5176

South Asian (SAS) AF: 0.282 AC: 1356 AN: 4816

European-Finnish (FIN) AF: 0.209 AC: 2212 AN: 10604

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18149 AN: 67980

Other (OTH) AF: 0.222 AC: 468 AN: 2108

Alfa AF: 0.244 Hom.: 1599

Bravo AF: 0.200

Asia WGS AF: 0.245 AC: 850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	9.7
DANN	Benign	0.94
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs1448901; hg19: chr2-207253640;