chr2-229744433-C-T

Position:

• chr2-229744433-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 0.319 in 152,118 control chromosomes in the GnomAD database, including 8,112 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 0.32 (8112 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.678

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 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: 0.319 AC: 48492 AN: 152000 Hom.: 8102 Cov.: 33

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.319 AC: 48532 AN: 152118 Hom.: 8112 Cov.: 33 AF XY: 0.313 AC XY: 23256 AN XY: 74368

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.318

Alfa AF: 0.304 Hom.: 11630

Bravo AF: 0.325

Asia WGS AF: 0.258 AC: 896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6707272; hg19: chr2-230609149; COSMIC: COSV53448533;