chr2-205680199-C-G

Variant names:

• chr2-205680199-C-G
• rs1400733

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.204 AC: 8450 AN: 41462

American (AMR) AF: 0.435 AC: 6650 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1425 AN: 3468

East Asian (EAS) AF: 0.518 AC: 2672 AN: 5162

South Asian (SAS) AF: 0.344 AC: 1661 AN: 4822

European-Finnish (FIN) AF: 0.347 AC: 3654 AN: 10544

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30026 AN: 67976

Other (OTH) AF: 0.404 AC: 847 AN: 2098

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
PhyloP100		-0.068

Splicing

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

Other links and lift over

dbSNP: rs1400733; hg19: chr2-206544923;