chr2-227952416-C-G

Position:

• chr2-227952416-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 0.13 in 152,106 control chromosomes in the GnomAD database, including 1,561 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 0.13 (1561 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.325 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: 0.130 AC: 19724 AN: 151988 Hom.: 1559 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.0616

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.0811

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.130 AC: 19748 AN: 152106 Hom.: 1561 Cov.: 32 AF XY: 0.131 AC XY: 9716 AN XY: 74366

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.0616

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.0805

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.113

Alfa AF: 0.101 Hom.: 570

Bravo AF: 0.133

Asia WGS AF: 0.174 AC: 604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10200894; hg19: chr2-228817132;