rs2320170

chr2-95574025-A-Gchr2-95574025-A-T

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 0.307 in 151,720 control chromosomes in the GnomAD database, including 7,967 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 0.31 (7967 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.85

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.399 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: 0.307 AC: 46555 AN: 151600 Hom.: 7945 Cov.: 31

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.307 AC: 46619 AN: 151720 Hom.: 7967 Cov.: 31 AF XY: 0.309 AC XY: 22914 AN XY: 74118

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.279

Alfa AF: 0.344 Hom.: 2042

Bravo AF: 0.306

Asia WGS AF: 0.252 AC: 873 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.011
Dann	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2320170; hg19: chr2-96239773;