chr2-9784258-A-G

Variant names:

• chr2-9784258-A-G
• rs2357266

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 0.665 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.665 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

Gnomad4 AFR AF: 0.745

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.508

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.687

Gnomad4 NFE AF: 0.636

Gnomad4 OTH AF: 0.627

Alfa AF: 0.633 Hom.: 70953

Bravo AF: 0.668

Asia WGS AF: 0.595 AC: 2071 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	0.93
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2357266; hg19: chr2-9924387;