rs2308

Positions:

• chr2-234763050-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;