chr2-228360409-C-T

Variant names:

• chr2-228360409-C-T
• rs6724689

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 0.185 in 151,972 control chromosomes in the GnomAD database, including 3,063 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 0.18 (3063 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.671
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.292 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: 0.185 AC: 28062 AN: 151856 Hom.: 3055 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.185 AC: 28100 AN: 151972 Hom.: 3063 Cov.: 32 AF XY: 0.186 AC XY: 13796 AN XY: 74268

African (AFR) AF: 0.297 AC: 12295 AN: 41440

American (AMR) AF: 0.153 AC: 2338 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0865 AC: 300 AN: 3470

East Asian (EAS) AF: 0.127 AC: 657 AN: 5166

South Asian (SAS) AF: 0.142 AC: 685 AN: 4808

European-Finnish (FIN) AF: 0.191 AC: 2017 AN: 10552

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

European-Non Finnish (NFE) AF: 0.138 AC: 9360 AN: 67964

Other (OTH) AF: 0.165 AC: 347 AN: 2108

Alfa AF: 0.169 Hom.: 282

Bravo AF: 0.185

Asia WGS AF: 0.136 AC: 472 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.0
DANN	Benign	0.28
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs6724689; hg19: chr2-229225125;