chr2-126902405-T-C

Position:

• chr2-126902405-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 0.253 in 152,152 control chromosomes in the GnomAD database, including 7,615 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 0.25 (7615 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 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: 0.252 AC: 38364 AN: 152032 Hom.: 7589 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.0742

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.253 AC: 38442 AN: 152152 Hom.: 7615 Cov.: 32 AF XY: 0.248 AC XY: 18449 AN XY: 74392

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.0742

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.250

Alfa AF: 0.199 Hom.: 780

Bravo AF: 0.275

Asia WGS AF: 0.258 AC: 898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.87
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6733840; hg19: chr2-127659981;