2-232539584-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.385 in 714,464 control chromosomes in the GnomAD database, including 55,866 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.36 (10316 hom., cov: 33)
  • Exomes 𝑓: 0.39 (45550 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.833

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BP6: Variant 2-232539584-C-G is Benign according to our data. Variant chr2-232539584-C-G is described in ClinVar as [Benign]. Clinvar id is 1293032.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 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: 0.358 AC: 54379 AN: 152052 Hom.: 10292 Cov.: 33

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.366

GnomAD4 exome AF: 0.392 AC: 220486 AN: 562296 Hom.: 45550 AF XY: 0.392 AC XY: 117815 AN XY: 300318

Gnomad4 AFR exome AF: 0.271

Gnomad4 AMR exome AF: 0.607

Gnomad4 ASJ exome AF: 0.375

Gnomad4 EAS exome AF: 0.565

Gnomad4 SAS exome AF: 0.430

Gnomad4 FIN exome AF: 0.332

Gnomad4 NFE exome AF: 0.357

Gnomad4 OTH exome AF: 0.381

GnomAD4 genome AF: 0.358 AC: 54440 AN: 152168 Hom.: 10316 Cov.: 33 AF XY: 0.360 AC XY: 26799 AN XY: 74374

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.556

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.372

Alfa AF: 0.212 Hom.: 475

Bravo AF: 0.371

Asia WGS AF: 0.525 AC: 1824 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Oct 02, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
Cadd	Benign	2.6
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11674608; hg19: chr2-233404294; COSMIC: COSV51328207;