2-205680199-C-G

Position:

• chr2-205680199-C-G

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 0.367 in 152,032 control chromosomes in the GnomAD database, including 11,087 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 0.37 (11087 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 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: 0.368 AC: 55830 AN: 151912 Hom.: 11089 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.367 AC: 55836 AN: 152032 Hom.: 11087 Cov.: 32 AF XY: 0.364 AC XY: 27031 AN XY: 74304

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.404

Alfa AF: 0.251 Hom.: 580

Bravo AF: 0.370

Asia WGS AF: 0.407 AC: 1413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1400733; hg19: chr2-206544923;