2-231599597-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 0.399 in 151,950 control chromosomes in the GnomAD database, including 13,096 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 (13096 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.484 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: 60648 AN: 151832 Hom.: 13091 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.399 AC: 60659 AN: 151950 Hom.: 13096 Cov.: 32 AF XY: 0.397 AC XY: 29472 AN XY: 74242

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.369

Alfa AF: 0.461 Hom.: 22440

Bravo AF: 0.388

Asia WGS AF: 0.350 AC: 1216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.3
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13384421; hg19: chr2-232464308;