chr2-239684069-A-G

Variant names:

• chr2-239684069-A-G
• rs1465820

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 0.458 in 152,014 control chromosomes in the GnomAD database, including 16,595 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 0.46 (16595 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.511
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 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: 0.458 AC: 69504 AN: 151896 Hom.: 16563 Cov.: 32

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.458 AC: 69582 AN: 152014 Hom.: 16595 Cov.: 32 AF XY: 0.468 AC XY: 34773 AN XY: 74296

African (AFR) AF: 0.486 AC: 20154 AN: 41458

American (AMR) AF: 0.586 AC: 8943 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1642 AN: 3470

East Asian (EAS) AF: 0.758 AC: 3919 AN: 5172

South Asian (SAS) AF: 0.601 AC: 2892 AN: 4814

European-Finnish (FIN) AF: 0.385 AC: 4071 AN: 10564

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26619 AN: 67950

Other (OTH) AF: 0.447 AC: 946 AN: 2114

Alfa AF: 0.411 Hom.: 20632

Bravo AF: 0.470

Asia WGS AF: 0.654 AC: 2274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.76
DANN	Benign	0.49
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs1465820; hg19: chr2-240605763;