rs792065

Variant names:

• chr2-5377390-G-A
• rs792065

Your query was ambiguous. Multiple possible variants found:

• chr2-5377390-G-A
• chr2-5377390-G-C

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 0.232 in 152,122 control chromosomes in the GnomAD database, including 4,819 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 0.23 (4819 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35289 AN: 152004 Hom.: 4819 Cov.: 33

Gnomad AFR AF: 0.0889

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.232 AC: 35288 AN: 152122 Hom.: 4819 Cov.: 33 AF XY: 0.234 AC XY: 17390 AN XY: 74342

Gnomad4 AFR AF: 0.0888

Gnomad4 AMR AF: 0.270

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.246

Alfa AF: 0.271 Hom.: 3375

Bravo AF: 0.227

Asia WGS AF: 0.314 AC: 1092 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs792065; hg19: chr2-5517523;