rs2308

Variant names:

• chr2-234763050-T-C
• rs2308

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 0.333 in 152,106 control chromosomes in the GnomAD database, including 12,095 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 0.33 (12095 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.836

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.66 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: 0.333 AC: 50577 AN: 151988 Hom.: 12066 Cov.: 33

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.333 AC: 50659 AN: 152106 Hom.: 12095 Cov.: 33 AF XY: 0.330 AC XY: 24553 AN XY: 74372

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.270

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.319

Alfa AF: 0.266 Hom.: 1251

Bravo AF: 0.360

Asia WGS AF: 0.455 AC: 1580 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.94
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2308; hg19: chr2-235671694;