2-9784258-A-G

Variant names:

• chr2-9784258-A-G
• rs2357266

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 0.665 in 152,196 control chromosomes in the GnomAD database, including 34,016 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 0.67 (34016 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.738 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: 0.665 AC: 101156 AN: 152078 Hom.: 33970 Cov.: 33

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.665 AC: 101258 AN: 152196 Hom.: 34016 Cov.: 33 AF XY: 0.665 AC XY: 49471 AN XY: 74410

African (AFR) AF: 0.745 AC: 30955 AN: 41528

American (AMR) AF: 0.689 AC: 10545 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1745 AN: 3472

East Asian (EAS) AF: 0.508 AC: 2630 AN: 5180

South Asian (SAS) AF: 0.601 AC: 2905 AN: 4832

European-Finnish (FIN) AF: 0.687 AC: 7269 AN: 10576

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.636 AC: 43277 AN: 68000

Other (OTH) AF: 0.627 AC: 1322 AN: 2110

Alfa AF: 0.641 Hom.: 148911

Bravo AF: 0.668

Asia WGS AF: 0.595 AC: 2071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.93
DANN	Benign	0.27
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs2357266; hg19: chr2-9924387;