2-127818257-C-T

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 0.127 in 151,772 control chromosomes in the GnomAD database, including 1,518 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 0.13 (1518 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19315 AN: 151676 Hom.: 1515 Cov.: 31

Gnomad AFR AF: 0.0676

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.127 AC: 19345 AN: 151772 Hom.: 1518 Cov.: 31 AF XY: 0.128 AC XY: 9509 AN XY: 74148

Gnomad4 AFR AF: 0.0679

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.150

Alfa AF: 0.0647 Hom.: 68

Bravo AF: 0.124

Asia WGS AF: 0.215 AC: 747 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.4
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2109312; hg19: chr2-128575831;