2-238212011-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 0.4 in 151,698 control chromosomes in the GnomAD database, including 13,808 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 0.40 (13808 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.629 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: 0.399 AC: 60527 AN: 151580 Hom.: 13773 Cov.: 30

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.400 AC: 60619 AN: 151698 Hom.: 13808 Cov.: 30 AF XY: 0.403 AC XY: 29887 AN XY: 74134

Gnomad4 AFR AF: 0.605

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.647

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.393

Alfa AF: 0.295 Hom.: 10116

Bravo AF: 0.418

Asia WGS AF: 0.464 AC: 1610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.2
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2341697; hg19: chr2-239120652;