2-226229029-T-C

Position:

• chr2-226229029-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 0.679 in 151,948 control chromosomes in the GnomAD database, including 35,250 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 0.68 (35250 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 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: 0.678 AC: 103008 AN: 151830 Hom.: 35212 Cov.: 31

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.679 AC: 103099 AN: 151948 Hom.: 35250 Cov.: 31 AF XY: 0.680 AC XY: 50464 AN XY: 74260

Gnomad4 AFR AF: 0.693

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.927

Gnomad4 SAS AF: 0.762

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.673

Alfa AF: 0.655 Hom.: 71140

Bravo AF: 0.689

Asia WGS AF: 0.847 AC: 2942 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2943641; hg19: chr2-227093745;