2-205680199-C-G

Variant names:

• chr2-205680199-C-G
• rs1400733

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;