rs7424145

chr2-210694812-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.0361

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.146

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.99
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7424145; hg19: chr2-211559536;