2-70447020-C-T

Variant names:

• chr2-70447020-C-T
• rs11466306

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 0.224 in 152,162 control chromosomes in the GnomAD database, including 4,300 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 0.22 (4300 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.423
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.286 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: 0.224 AC: 34049 AN: 152044 Hom.: 4292 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.224 AC: 34061 AN: 152162 Hom.: 4300 Cov.: 33 AF XY: 0.224 AC XY: 16681 AN XY: 74376

African (AFR) AF: 0.124 AC: 5166 AN: 41528

American (AMR) AF: 0.154 AC: 2348 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 720 AN: 3472

East Asian (EAS) AF: 0.299 AC: 1545 AN: 5174

South Asian (SAS) AF: 0.230 AC: 1107 AN: 4822

European-Finnish (FIN) AF: 0.309 AC: 3263 AN: 10560

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19096 AN: 68002

Other (OTH) AF: 0.224 AC: 473 AN: 2114

Alfa AF: 0.248 Hom.: 2067

Bravo AF: 0.208

Asia WGS AF: 0.286 AC: 994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs11466306; hg19: chr2-70674152;