rs7424145

Variant names:

• chr2-210694812-G-A
• rs7424145

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 0.155 in 151,926 control chromosomes in the GnomAD database, including 2,293 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 0.16 (2293 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23592 AN: 151808 Hom.: 2290 Cov.: 32

Gnomad AFR AF: 0.0361

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.155 AC: 23593 AN: 151926 Hom.: 2293 Cov.: 32 AF XY: 0.162 AC XY: 12015 AN XY: 74226

African (AFR) AF: 0.0361 AC: 1497 AN: 41482

American (AMR) AF: 0.204 AC: 3099 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 574 AN: 3466

East Asian (EAS) AF: 0.158 AC: 813 AN: 5156

South Asian (SAS) AF: 0.185 AC: 890 AN: 4820

European-Finnish (FIN) AF: 0.303 AC: 3206 AN: 10576

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12993 AN: 67884

Other (OTH) AF: 0.146 AC: 308 AN: 2108

Alfa AF: 0.177 Hom.: 351

Bravo AF: 0.144

Asia WGS AF: 0.171 AC: 596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.99
DANN	Benign	0.68
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs7424145; hg19: chr2-211559536;