2-227952416-C-G

Variant names:

• chr2-227952416-C-G
• rs10200894

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 0.13 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.153 AC: 6356 AN: 41486

American (AMR) AF: 0.153 AC: 2343 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0616 AC: 214 AN: 3472

East Asian (EAS) AF: 0.338 AC: 1745 AN: 5162

South Asian (SAS) AF: 0.0805 AC: 388 AN: 4818

European-Finnish (FIN) AF: 0.141 AC: 1488 AN: 10588

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6879 AN: 68000

Other (OTH) AF: 0.113 AC: 239 AN: 2108

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
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs10200894; hg19: chr2-228817132;