chr2-9784258-A-G

Position:

• chr2-9784258-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;